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  • 451.
    Hedenstierna-Jonson, Charlotte
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology. Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Kjellström, Anna
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden .
    Zachrisson, Torun
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Krzewińska, Maja
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Sobrado, Veronica
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Price, Neil
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Götherström, Anders
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Storå, Jan
    Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    A female Viking warrior confirmed by genomics2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 164, no 4, p. 853-860Article in journal (Refereed)
    Abstract [en]

    OBJECTIVES: The objective of this study has been to confirm the sex and the affinity of an individual buried in a well-furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context. A genomic confirmation of the biological sex of the individual was considered necessary to solve the issue.

    MATERIALS AND METHODS: Genome-wide sequence data was generated in order to confirm the biological sex, to support skeletal integrity, and to investigate the genetic relationship of the individual to ancient individuals as well as modern-day groups. Additionally, a strontium isotope analysis was conducted to highlight the mobility of the individual.

    RESULTS: The genomic results revealed the lack of a Y-chromosome and thus a female biological sex, and the mtDNA analyses support a single-individual origin of sampled elements. The genetic affinity is close to present-day North Europeans, and within Sweden to the southern and south-central region. Nevertheless, the Sr values are not conclusive as to whether she was of local or nonlocal origin.

    DISCUSSION: The identification of a female Viking warrior provides a unique insight into the Viking society, social constructions, and exceptions to the norm in the Viking time-period. The results call for caution against generalizations regarding social orders in past societies.

  • 452. Hedren, Mikael
    et al.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A replacement name for a species of Hypoestes (Acanthaceae) from Somalia2015In: Willdenowia, ISSN 0511-9618, E-ISSN 1868-6397, Vol. 45, no 1, p. 93-93Article in journal (Refereed)
    Abstract [en]

    Hypoestes canescens Hedren & Thulin, nom. nov., is proposed for the illegitimate name H. cinerea Hedren, non C. B. Clarke.

  • 453.
    Hehenberger, Elisabeth
    et al.
    Univ British Columbia, Dept Bot, Canadian Inst Adv Res, Vancouver, BC, Canada..
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ British Columbia, Dept Bot, Canadian Inst Adv Res, Vancouver, BC, Canada..
    Kolisko, Martin
    Univ British Columbia, Dept Bot, Canadian Inst Adv Res, Vancouver, BC, Canada..
    Keeling, Patrick J.
    Univ British Columbia, Dept Bot, Canadian Inst Adv Res, Vancouver, BC, Canada..
    Functional Relationship between a Dinoflagellate Host and Its Diatom Endosymbiont2016In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 9, p. 2376-2390Article in journal (Refereed)
    Abstract [en]

    While we know much about the evolutionary patterns of endosymbiotic organelle origins, we know less about how the actual process unfolded within each system. This is partly due to the massive changes endosymbiosis appears to trigger, and partly because most organelles evolved in the distant past. The dinotoms are dinoflagellates with diatom endosymbionts, and they represent a relatively recent but nevertheless obligate endosymbiotic association. We have carried out deep sequencing of both the host and endosymbiont transcriptomes from two dinotoms, Durinskia baltica and Glenodinium foliaceum, to examine how the nucleocytosolic compartments have functionally integrated. This analysis showed little or no functional reduction in either the endosymbiont or host, and no evidence for genetic integration. Rather, host and endosymbiont seem to be bound to each other via metabolites, such as photosynthate exported from the endosymbiont to the host as indicated by the presence of plastidic phosphate translocators in the host transcriptome. The host is able to synthesize starch, using plant-specific starch synthases, as a way to store imported photosynthate.

  • 454.
    Hendriks, Hester S.
    et al.
    Utrecht University.
    Koolen, Lucas A. E.
    Utrecht University.
    Dingemans, Milou M. L.
    Utrecht University.
    Viberg, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Lee, Iwa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Leonards, Pim E.G.
    VU University, Amsterdam.
    Ramakers, Geert M.J.
    University Medical Center Utrecht.
    Westerink, Remco H.S.
    Utrecht University.
    Effects on neonatal exposure to the flame retardant tetrabrombisphenol-A, aluminum diethylphosphinate or zinc stannate on long-term, potentiation and synaptic protein levels in mice2014In: Archives of Toxicology, ISSN 0340-5761, E-ISSN 1432-0738, Vol. 89, no 12, p. 2345-2354Article in journal (Refereed)
    Abstract [en]

    Brominated flame retardants such as tetrabromobisphenol-A (TBBPA) may exert (developmental) neurotoxic effects. However, data on (neuro)toxicity of halogen-free flame retardants (HFFRs) are scarce. Recent in vitro studies indicated a high neurotoxic potential for some HFFRs, e.g., zinc stannate (ZS), whereas the neurotoxic potential of other HFFRs, such as aluminum diethylphosphinate (Alpi), appears low. However, the in vivo (neuro)toxicity of these compounds is largely unknown. We therefore investigated effects of neonatal exposure to TBBPA, Alpi or ZS on synaptic plasticity in mouse hippocampus. Male C57bl/6 mice received a single oral dose of 211 µmol/kg bw TBBPA, Alpi or ZS on postnatal day (PND) 10. On PND 17–19, effects on hippocampal synaptic plasticity were investigated using ex vivo extracellular field recordings. Additionally, we measured levels of postsynaptic proteins involved in long-term potentiation (LTP) as well as flame retardant concentrations in brain, muscle and liver tissues. All three flame retardants induced minor, but insignificant, effects on LTP. Additionally, TBBPA induced a minor decrease in post-tetanic potentiation. Despite these minor effects, expression of selected synaptic proteins involved in LTP was not affected. The flame retardants could not be measured in significant amounts in the brains, suggesting low bioavailability and/or rapid elimination/metabolism. We therefore conclude that a single neonatal exposure on PND 10 to TBBPA, Alpi or ZS does affect neurodevelopment and synaptic plasticity only to a small extent in mice. Additional data, in particular on persistence, bioaccumulation and (in vivo) toxicity, following prolonged (developmental) exposure are required for further (human) risk assessment.

  • 455. Hendriks, Hester S.
    et al.
    van Kleef, Regina G. D. M.
    Dingemans, Milou M. L.
    Meijer, Mareike
    Muilwijk, Mirthe
    van den Berg, Martin
    Ramakers, Geert M.
    Koolen, Lucas A.
    Leonards, Pim E.
    Viberg, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Lee, Iwa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Westerink, Remco H. S.
    Neurotoxicity assessment of 15 brominated- and halogen-free flame retardants2015In: Neurotoxicology and Teratology, ISSN 0892-0362, E-ISSN 1872-9738, Vol. 49, p. 106-107Article in journal (Other academic)
  • 456.
    Herbin, Marc
    et al.
    Muséum National d'Histoire Naturelle, Paris, France.
    Dupret, Vincent
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Goussard, Florent
    Muséum National d'Histoire Naturelle, paris, France.
    Clément, Gaël
    Muséum National d'Histoire Naturelle, Paris, France.
    Les techniques d’imagerie 3D au service de la valorisation scientifique des collections anatomiques2010In: La Lettre de l'OCIM, ISSN 0994-1908, Vol. 131, p. 13-18Article in journal (Refereed)
    Abstract [en]

    The presentation of this virtual study of the anatomy of a Coelacanthe specimen produced using three dimensional x ray imaging and magnetic resonance notably brings light to the possibilities of application of these technologies – which avoid repetitive manipulations and preserve the morphological integrity of precious and scientifically important specimens – in the field of scenography or of preventive conservation.

  • 457.
    Herrmann, Björn
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Isaksson, Jenny
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tangrot, Jeanette
    Saleh, Isam
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Versteeg, Bart
    Gravningen, Kirsten
    Bruisten, Sylvia
    Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries2015In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 53, no 7, p. 2172-2179Article in journal (Refereed)
    Abstract [en]

    The Uppsala University Chlamydia trachomatis multilocus sequence type (MLST) database (http://mlstdb.bmc.uu.se) is based on five target regions (non-housekeeping genes) and the ompA gene. Each target has various numbers of alleles-hctB, 89; CT058, 51; CT144, 30; CT172, 38; and pbpB, 35-derived from 13 studies. Our aims were to perform an overall analysis of all C. trachomatis MLST sequence types (STs) in the database, examine STs with global spread, and evaluate the phylogenetic capability by using the five targets. A total of 415 STs were recognized from 2,089 specimens. The addition of 49 ompA gene variants created 459 profiles. ST variation and their geographical distribution were characterized using eBURST and minimum spanning tree analyses. There were 609 samples from men having sex with men (MSM), with 4 predominating STs detected in this group, comprising 63% of MSM cases. Four other STs predominated among 1,383 heterosexual cases comprising, 31% of this group. The diversity index in ocular trachoma cases was significantly lower than in sexually transmitted chlamydia infections. Predominating STs were identified in 12 available C. trachomatis whole genomes which were compared to 22 C. trachomatis full genomes without predominating STs. No specific gene in the 12 genomes with predominating STs could be linked to successful spread of certain STs. Phylogenetic analysis showed that MLST targets provide a tree similar to trees based on whole-genome analysis. The presented MLST scheme identified C. trachomatis strains with global spread. It provides a tool for epidemiological investigations and is useful for phylogenetic analyses.

  • 458.
    Herrmann, Björn
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Stolt, Pelle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Abdeldaim, Guma
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Kirsebom, Leif A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Thollesson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Differentiation and Phylogenetic Relationships in Mycobacterium spp with Special Reference to the RNase P RNA Gene rnpB2014In: Current Microbiology, ISSN 0343-8651, E-ISSN 1432-0991, Vol. 69, no 5, p. 634-639Article in journal (Refereed)
    Abstract [en]

    The rnpB gene encodes for the RNA subunit of the catalytic ribonuclease RNase P and is present in all bacteria and has both conserved and highly variable sequence regions. Determination of rnpB in 35 Mycobacterium spp. showed species specific sequences for all species except the Mycobacterium tuberculosis complex (four species). High sequence variation was seen in the P3, P15 and P19 regions of suggested secondary structures of the corresponding RNase P RNA molecules. Phylogenetic analysis showed that rnpB gave similar tree topologies as 16S rRNA and hsp65 genes. A combined analysis of the three genes increased the number of nodes with significant support from 10 to 19. The results indicate that rnpB is useful for phylogenetic studies and is a possible target for identification and detection of Mycobacterium spp.

  • 459.
    Hervella, M.
    et al.
    Univ Basque Country UPV EHU, Dept Genet Phys Anthropol & Anim Physiol, Barrio Sarriena S-N, Leioa 48940, Bizkaia, Spain..
    Svensson, Emma M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Alberdi, A.
    Univ Copenhagen, Nat Hist Museum Denmark, Oster Voldgade 5-7, DK-1350 Copenhagen, Denmark..
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Izagirre, N.
    Univ Basque Country UPV EHU, Dept Genet Phys Anthropol & Anim Physiol, Barrio Sarriena S-N, Leioa 48940, Bizkaia, Spain..
    Munters, Arielle R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Alonso, S.
    Univ Basque Country UPV EHU, Dept Genet Phys Anthropol & Anim Physiol, Barrio Sarriena S-N, Leioa 48940, Bizkaia, Spain..
    Ioana, M.
    Univ Med & Pharm Craiova, Human Genom Lab, Bvd 1 Mai 66, Craiova, Romania.;Radboud Univ Nijmegen, Med Ctr, Dept Internal Med, NL-6525 ED Nijmegen, Netherlands.;Radboud Univ Nijmegen, Med Ctr, Radboud Ctr Infect Dis, NL-6525 ED Nijmegen, Netherlands..
    Ridiche, F.
    Museum Oltenia, Hist & Archaeol Dept, Madona Dudu Str 14, Craiova, Romania..
    Soficaru, A.
    Romanian Acad, Fr J Rainer Inst Anthropol, Eroii Sanitari 8,POB 35-13, Bucharest, Romania..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Netea, M. G.
    Radboud Univ Nijmegen, Med Ctr, Dept Internal Med, NL-6525 ED Nijmegen, Netherlands.;Radboud Univ Nijmegen, Med Ctr, Radboud Ctr Infect Dis, NL-6525 ED Nijmegen, Netherlands..
    de-la-Rua, C.
    Univ Basque Country UPV EHU, Dept Genet Phys Anthropol & Anim Physiol, Barrio Sarriena S-N, Leioa 48940, Bizkaia, Spain..
    The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 25501Article in journal (Refereed)
    Abstract [en]

    After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Pestera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.

  • 460.
    Hiiesalu, Indrek
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    Plant species richness and productivity determine the diversity of soil fungal guilds in temperate coniferous forest and bog habitats2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 18, p. 4846-4858Article in journal (Refereed)
    Abstract [en]

    Fungi have important roles as decomposers, mycorrhizal root symbionts and pathogens in forest ecosystems, but there is limited information about their diversity and composition at the landscape scale. This work aimed to disentangle the factors underlying fungal richness and composition along the landscape-scale moisture, organic matter and productivity gradients. Using high-throughput sequencing, we identified soil fungi from 54 low-productivity Pinus sylvestris-dominated plots across three study areas in Estonia and determined the main predictors of fungal richness based on edaphic, floristic and spatial variables. Fungal richness displayed unimodal relationship with organic matter and deduced soil moisture. Plant richness and productivity constituted the key predictors for taxonomic richness of functional guilds. Composition of fungi and the main ectomycorrhizal fungal lineages and hyphal exploration types was segregated by moisture availability and soil nitrogen. We conclude that plant productivity and diversity determine the richness and proportion of most functional groups of soil fungi in low-productive pine forests on a landscape scale. Adjacent stands of pine forest may differ greatly in the dominance of functional guilds that have marked effects on soil carbon and nitrogen cycling in these forest ecosystems.

  • 461. Hill, M. S.
    et al.
    Hill, A. L.
    Lopez, J.
    Peterson, K. J.
    Pomponi, S.
    Diaz, M. C.
    Thacker, R. W.
    Adamska, M.
    Boury-Esnault, N.
    Cárdenas, Paco
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Chaves-Fonnegra, A.
    Danka, E.
    De Laine, B. -O
    Formica, D.
    Hajdu, E.
    Lobo-Hajdu, G.
    Klontz, S.
    Morrow, C. C.
    Patel, J.
    Picton, B.
    Pisani, D.
    Pohlmann, D.
    Redmond, N. E.
    Reed, J.
    Richey, S.
    Riesgo, A.
    Rubin, E.
    Russell, Z.
    Rützler, K.
    Sperling, E. A.
    di Stefano, M.
    Tarver, J. E.
    Collins, A. G.
    Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 1, p. e50437-Article in journal (Refereed)
    Abstract [en]

    Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well-supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets.

  • 462.
    Hill, Tobias
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Nordström, Karl J V
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Thollesson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Säfström, Tommy M
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Vernersson, Andreas K E
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Fredriksson, Robert
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Schiöth, Helgi B
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees2010In: BMC Evolutionary Biology, ISSN 1471-2148, Vol. 10, no 1, p. 42-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Phylogenetic trees based on sequences from a set of taxa can be incongruent due to horizontal gene transfer (HGT). By identifying the HGT events, we can reconcile the gene trees and derive a taxon tree that adequately represents the species' evolutionary history. One HGT can be represented by a rooted Subtree Prune and Regraft (RSPR) operation and the number of RSPRs separating two trees corresponds to the minimum number of HGT events. Identifying the minimum number of RSPRs separating two trees is NP-hard, but the problem can be reduced to fixed parameter tractable. A number of heuristic and two exact approaches to identifying the minimum number of RSPRs have been proposed. This is the first implementation delivering an exact solution as well as the intermediate trees connecting the input trees. RESULTS: We present the SPR Identification Tool (SPRIT), a novel algorithm that solves the fixed parameter tractable minimum RSPR problem and its GPL licensed Java implementation. The algorithm can be used in two ways, exhaustive search that guarantees the minimum RSPR distance and a heuristic approach that guarantees finding a solution, but not necessarily the minimum one. We benchmarked SPRIT against other software in two different settings, small to medium sized trees i.e. five to one hundred taxa and large trees i.e. thousands of taxa. In the small to medium tree size setting with random artificial incongruence, SPRIT's heuristic mode outperforms the other software by always delivering a solution with a low overestimation of the RSPR distance. In the large tree setting SPRIT compares well to the alternatives when benchmarked on finding a minimum solution within a reasonable time. SPRIT presents both the minimum RSPR distance and the intermediate trees. CONCLUSIONS: When used in exhaustive search mode, SPRIT identifies the minimum number of RSPRs needed to reconcile two incongruent rooted trees. SPRIT also performs quick approximations of the minimum RSPR distance, which are comparable to, and often better than, purely heuristic solutions. Put together, SPRIT is an excellent tool for identification of HGT events and pinpointing which taxa have been involved in HGT.

  • 463.
    Hilonga, S.
    et al.
    Muhimbili Univ Hlth & Allied Sci, Inst Tradit Med, POB 65001, Dar Es Salaam, Tanzania.
    Otieno, J. N.
    Muhimbili Univ Hlth & Allied Sci, Inst Tradit Med, POB 65001, Dar Es Salaam, Tanzania.
    Ghorbani, Abdolbaset
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Pereus, D.
    Muhimbili Univ Hlth & Allied Sci, Inst Tradit Med, POB 65001, Dar Es Salaam, Tanzania.
    Kocyan, A.
    Univ Potsdam, Biodivers Res Systemat Bot, D-14469 Potsdam, Germany.
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Oslo, Nat Hist Museum, POB 1172, NO-0318 Oslo, Norway.
    Trade of wild-harvested medicinal plant species in local markets of Tanzania and its implications for conservation2019In: South African Journal of Botany, ISSN 0254-6299, E-ISSN 1727-9321, Vol. 122, p. 214-224Article in journal (Refereed)
    Abstract [en]

    In Tanzania, about 10% of the reported 12,000 species of higher plants are estimated to be used as medicine for treating different human health problems. Most of the medicinal plants are collected from wild populations, but their trade and quantities are not properly recorded. Monitoring of trade in wild-harvested medicinal plants is challenging asmostmaterials are traded in various processed forms and most vendors practice informal trade. Yet, monitoring is important for conservation and sustainability. This study aims to assess the trade of wild-harvested medicinal plant species in local markets of Tanzania and its implications for conservation. Semi-structured interviews were used to record frequency, volume of trade and uses of wild-harvested medicinal plants in Arusha, Dodoma, Mbeya, Morogoro and Mwanza regions. Relative frequency of citation and informant consensus factor were calculated for each species and mentioned use category. Forty vendors were interviewed, and 400 out of 522 collected market samples were identified to 162 species from herbarium-deposited collections. Plant parts with the largest volume of trade were roots (3818 kg), bark (1163 kg) and leaves (492 kg). The most frequently traded species were Zanthoxylum chalybaeum Engl., Albizia anthelmintica Brongn., Zanha africana (Radlk.) Exell, Warburgia stuhlmannii and Vachellia nilotica (L.) P.J.H. Hurter & Mabb. The most popular medicinal plants in the markets are connected to local health problems including malaria, libido disorders or infertility. The high diversity of commercialized plants used for medicinal issues mainly relies on wild stock for local consumption and international trade, and this has significant implications for conservation concerns. (C) 2018 SAAB. Published by Elsevier B.V. All rights reserved.

  • 464.
    Hiltunen, Markus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Grudzinska-Sterno, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Wallerman, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 16, p. 2758-2765Article in journal (Refereed)
    Abstract [en]

    Most mutations in coding regions of the genome are deleterious, causing selection to favor mechanisms that minimize the mutational load over time [1-5]. DNA replication during cell division is a major source of new mutations. It is therefore important to limit the number of cell divisions between generations, particularly for large and long-lived organisms [6-9]. The germline cells of animals and the slowly dividing cells in plant meristems are adaptations to control the number of mutations that accumulate over generations [9-11]. Fungi lack a separated germline while harboring species with very large and long-lived individuals that appear to maintain highly stable genomes within their mycelia [8, 12, 13]. Here, we studied genomic mutation accumulation in the fairy-ring mushroom Marasmius oreades. We generated a chromosome-level genome assembly using a combination of cutting-edge DNA sequencing technologies and resequenced 40 samples originating from six individuals of this fungus. The low number of mutations recovered in the sequencing data suggests the presence of an unknown mechanism that works to maintain extraordinary genome integrity over vegetative growth in M. oreades. The highly structured growth pattern of M. oreades allowed us to estimate the number of cell divisions leading up to each sample [14, 15], and from this data, we infer an incredibly low per mitosis mutation rate (3.8 x 10(-12) mutations per site and cell division) as one of several possible explanations for the low number of identified mutations.

  • 465.
    Hinsley, Amy
    et al.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Univ Oxford, Radcliffe Observ Quarter, Dept Zool, Woodstock Rd, Oxford OX1 3PS, England..
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Univ Oslo, Nat Hist Museum, POB 1172 Blindern, N-0318 Oslo, Norway..
    Fay, Michael F.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Royal Bot Gardens, Conservat Sci, Richmond TW7 3AE, Surrey, England.;Univ Western Australia, Sch Biol Sci, 35 Stirling Highway, Perth, WA 6009, Australia..
    Gale, Stephan W.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Kadoorie Farm & Bot Garden, Lam Kam Rd, Tai Po, Hong Kong, Peoples R China..
    Gardiner, Lauren M.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Royal Bot Gardens, Conservat Sci, Richmond TW7 3AE, Surrey, England.;Cambridge Univ Bot Gardens, Dept Plant Sci, Sainsbury Lab, Cambridge Univ Herbarium, Bateman St, Cambridge CB2 1LR, England..
    Gunasekara, Rajasinghe S.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Sri Lanka Customs, 40 Main St, Colombo 11, Sri Lanka..
    Kumar, Pankaj
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Kadoorie Farm & Bot Garden, Lam Kam Rd, Tai Po, Hong Kong, Peoples R China..
    Masters, Susanne
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Nat Biodivers Ctr, Darwinweg 2, NL-2333 CR Leiden, Netherlands.;Leiden Univ, Rapenburg 70, NL-2311 EZ Leiden, Netherlands..
    Metusala, Destario
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Indonesian Inst Sci LIPI, Purwodadi Bot Garden, Jalan Raya Surabaya Malang KM-65, Pasuruan 67163, Jawa Timur, Indonesia..
    Roberts, David L.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Univ Kent, Sch Anthropol & Conservat, Durrell Inst Conservat & Ecol, Marlowe Bldg, Canterbury CT2 7NR, Kent, England..
    Veldman, Sarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England..
    Wong, Shan
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Univ Oxford, Sch Geog & Environm, South Parks Rd, Oxford OX1 3QY, England..
    Phelps, Jacob
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Univ Lancaster, Lancaster Environm Ctr, Lib Ave, Lancaster LA1 4YQ, England..
    A review of the trade in orchids and its implications for conservation2018In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 186, no 4, p. 435-455Article, review/survey (Refereed)
    Abstract [en]

    Orchids are one of the largest plant families and are commercially traded for a variety of purposes, including as ornamental plants, medicinal products and food. These markets involve thousands of species, which may be traded legally or illegally, sustainably or unsustainably, and take place at local, national or international scales. In this review, we provide the first overview of commercial orchid trade globally and highlight the main types that involve wild-collected plants. Much of this trade is the result of illegal harvest meaning that it is little documented and is absent from official statistics, at the same time as being of growing conservation concern. We discuss the associated legal-regulatory context, identify key conservation challenges and highlight four key priorities for addressing these challenges. These are to (1) research trade dynamics and the impacts of harvest; (2) strengthen the legal trade of orchids; (3) adopt measures to reduce illegal trade; and (4) raise the profile of orchid trade among policy makers, conservationists and the public.

  • 466.
    Histon, Kathleen
    et al.
    University of Modena.
    Zigaite, ZivileUppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Evolutionary palaeoecology and palaeobiogeography2014Collection (editor) (Refereed)
  • 467.
    Histon, Kathleen
    et al.
    University of Modena.
    Zigaite, Zivile
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Preface2015In: Estonian journal of earth sciences, ISSN 1736-4728, E-ISSN 1736-7557, Vol. 64, no 1, p. 1-2Article in journal (Other academic)
    Abstract [en]

    Evolutionary palaeoecology and palaeobiogeography: year 4 of the IGCP-591 project 'The Early to Middle Palaeozoic Revolution - Bridging the Gap between the Great Ordovician Biodiversification Event and the Devonian Terrestrial Revolution

  • 468.
    Hjalmarsson, Marie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Tooke, Nigel
    Brunström, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Effects of ethinylestradiol on DNA methylation in a 5-prime flanking region of the vitellogenin I gene in adult zebrafish (Danio rerio)2010In: Toxicology letters, 2010, Vol. 196, p. S117-Conference paper (Refereed)
  • 469.
    Hladik, Daniela
    et al.
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Inst Radiat Biol, D-85764 Neuherberg, Germany;Tech Univ Munich, Chair Radiat Biol, D-80333 Munich, Germany.
    Buratovic, Sonja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Von Toerne, Christine
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Res Unit Prot Sci, D-80939 Munich, Germany.
    Azimzadeh, Omid
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Inst Radiat Biol, D-85764 Neuherberg, Germany.
    Subedi, Prabal
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Inst Radiat Biol, D-85764 Neuherberg, Germany.
    Philipp, Jos
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Inst Radiat Biol, D-85764 Neuherberg, Germany.
    Winkler, Stefanie
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Inst Radiat Biol, D-85764 Neuherberg, Germany.
    Feuchtinger, Annette
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Res Unit Analyt Pathol, D-85764 Neuherberg, Germany.
    Samson, Elenore
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Res Unit Analyt Pathol, D-85764 Neuherberg, Germany.
    Hauck, Stefanie M.
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Res Unit Prot Sci, D-80939 Munich, Germany.
    Stenerlöw, Bo
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medical Radiation Science.
    Eriksson, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Atkinson, Michael J.
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Inst Radiat Biol, D-85764 Neuherberg, Germany;Tech Univ Munich, Chair Radiat Biol, D-80333 Munich, Germany.
    Tapio, Soile
    German Res Ctr Environm Hlth GmbH HMGU, Helmholtz Zentrum Munchen, Inst Radiat Biol, D-85764 Neuherberg, Germany.
    Combined Treatment with Low-Dose Ionizing Radiation and Ketamine Induces Adverse Changes in CA1 Neuronal Structure in Male Murine Hippocampi2019In: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 20, no 23, article id 6103Article in journal (Refereed)
    Abstract [en]

    In children, ketamine sedation is often used during radiological procedures. Combined exposure of ketamine and radiation at doses that alone did not affect learning and memory induced permanent cognitive impairment in mice. The aim of this study was to elucidate the mechanism behind this adverse outcome. Neonatal male NMRI mice were administered ketamine (7.5 mg kg(-1)) and irradiated (whole-body, 100 mGy or 200 mGy, Cs-137) one hour after ketamine exposure on postnatal day 10. The control mice were injected with saline and sham-irradiated. The hippocampi were analyzed using label-free proteomics, immunoblotting, and Golgi staining of CA1 neurons six months after treatment. Mice co-exposed to ketamine and low-dose radiation showed alterations in hippocampal proteins related to neuronal shaping and synaptic plasticity. The expression of brain-derived neurotrophic factor, activity-regulated cytoskeleton-associated protein, and postsynaptic density protein 95 were significantly altered only after the combined treatment (100 mGy or 200 mGy combined with ketamine, respectively). Increased numbers of basal dendrites and branching were observed only after the co-exposure, thereby constituting a possible reason for the displayed alterations in behavior. These data suggest that the risk of radiation-induced neurotoxic effects in the pediatric population may be underestimated if based only on the radiation dose.

  • 470.
    Hoffman, Tove
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lindeborg, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine.
    Barboutis, Christos
    Hellen Ornithol Soc Birdlife, Athens, Greece.
    Erciyas-Yavuz, Kiraz
    Ondokuz Mayis Univ, Samsun, Turkey.
    Evander, Magnus
    Umea Univ, Umea, Sweden.
    Fransson, Thord
    Swedish Museum Nat Hist, Stockholm, Sweden.
    Figuerola, Jordi
    Estn Biol Donana, Seville, Spain;Ciber Epidemil & Salud Publ, Madrid, Spain.
    Jaenson, Thomas G.T.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kiat, Yosef
    Hebrew Univ Jerusalem, Jerusalem, Israel.
    Lindgren, Per-Eric
    Linkoping Univ, Linkoping, Sweden.
    Lundkvist, Åke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Mohamed, Nahla
    Umea Univ, Umea, Sweden.
    Moutailler, Sara
    Agence Natl Secur Sanit Alimentat, Maisons Alfort, France.
    Nystrom, Fredrik
    Linkoping Univ, Linkoping, Sweden.
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine.
    Salaneck, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine.
    Alkhurma Hemorrhagic Fever Virus RNA in Hyalomma rufipes Ticks Infesting Migratory Birds, Europe and Asia Minor2018In: Emerging Infectious Diseases, ISSN 1080-6040, E-ISSN 1080-6059, Vol. 24, no 5, p. 879-882Article in journal (Refereed)
    Abstract [en]

    Alkhurma hemorrhagic fever virus RNA was detected in immature Hyalomma rufipes ticks infesting northward migratory birds caught in the North Mediterranean Basin. This finding suggests a role for birds in the ecology of the Alkhurma hemorrhagic fever virus and a potential mechanism for dissemination to novel regions. Increased surveillance is warranted.

  • 471.
    Holland, Linda Z.
    et al.
    Univ Calif San Diego, Scripps Inst Oceanog, Marine Biol Res Div, La Jolla, CA 92093 USA.
    Ocampo Daza, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Univ Calif Merced, Sch Nat Sci, Merced, CA 95343 USA.
    A new look at an old question: when did the second whole genome duplication occur in vertebrate evolution?2018In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 19, article id 209Article in journal (Refereed)
    Abstract [en]

    A recent study used 61 extant animal genomes to reconstruct the chromosomes of the hypothetical amniote ancestor. Comparison of this karyotype to the 17 chordate linkage groups previously inferred in the ancestral chordate indicated that two whole genome duplications probably occurred in the lineage preceding the ancestral vertebrate.

  • 472.
    Hollfelder, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Population genetic history and patterns of admixture: Examples from northeastern and southern Africa2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The origin of humans lies in Africa, as has been shown by archaeology, paleontology and genetics. Here, we can find the largest genetic diversity and the deepest split among human populations. African genetic diversity has been shaped by a long and complex history. In this thesis, I applied population genomic methods to investigate different aspects of the demographic history of Africa, specifically northeast and southern Africa.

    Both of these regions are population melting-pots, with many historically known major migrations.

    In northeast African populations, Eurasian admixture in central, northern, and eastern Sudanese populations was identified to be of Middle Eastern origin and the admixture time coincides with the Arab expansion. In northeast Africa I also studied alleles associated with lactase persistence, the ability to digest milk at an adult age. A wide diversity of these alleles was detected in Sudan, most commonly among pastoralists. The presence of a Middle Eastern LP-allele and absence of a European LP-allele is consistent with the admixture pattern observed in the first paper.

    I deciphered the patterns of genetic admixture in the Afrikaner population of South Africa and compared admixture patterns of the X-chromosome and autosomes to disentangle sex-biased admixture in southern African populations.

    The Afrikaner were shown to carry on average 5% non-European admixture, mostly from Khoe-San, East and South Asian sources. The admixture was sex-biased, with larger contributions from European males and admixture with Africans can be dated to 9-10 generations ago – fitting previous genealogical estimates of the age and the history of the population.

    Bantu-speaker/Khoe-San contact shows a pattern of female Bantu-speaker bias, which is conflicting with previous mtDNA and Y-chromosome studies. A change in mate-choice over time could explain this discrepancy.

    This thesis contributes to a deeper understanding of African demographic history in general and of some previously understudied populations and geographic areas in particular.

    List of papers
    1. Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations
    Open this publication in new window or tab >>Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations
    Show others...
    2017 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, no 8, article id e1006976Article in journal (Refereed) Published
    Abstract [en]

    Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gateway out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping similar to 3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400-200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.

    Place, publisher, year, edition, pages
    PUBLIC LIBRARY SCIENCE, 2017
    National Category
    Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-333162 (URN)10.1371/journal.pgen.1006976 (DOI)000408763800042 ()28837655 (PubMedID)
    Available from: 2017-11-07 Created: 2017-11-07 Last updated: 2017-12-13Bibliographically approved
    2. The genetic variation of lactase persistence alleles in northeast Africa
    Open this publication in new window or tab >>The genetic variation of lactase persistence alleles in northeast Africa
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-336177 (URN)
    Available from: 2017-12-12 Created: 2017-12-12 Last updated: 2017-12-13
    3. Patterns of African and Asian admixture in the Afrikaner population of South Africa
    Open this publication in new window or tab >>Patterns of African and Asian admixture in the Afrikaner population of South Africa
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-335377 (URN)
    Available from: 2017-12-04 Created: 2017-12-04 Last updated: 2017-12-13
    4. Genetic patterns of sex-biased admixture in southern African populations
    Open this publication in new window or tab >>Genetic patterns of sex-biased admixture in southern African populations
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-335212 (URN)
    Available from: 2017-12-01 Created: 2017-12-01 Last updated: 2017-12-13
  • 473.
    Hollfelder, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Babiker, Hiba
    Granehäll, Lena
    Schlebusch, Carina Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The genetic variation of lactase persistence alleles in northeast AfricaManuscript (preprint) (Other academic)
  • 474.
    Hollfelder, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Erasmus, Johannes Christoff
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Greeff, Jaco M
    Schlebusch, Carina Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Patterns of African and Asian admixture in the Afrikaner population of South AfricaManuscript (preprint) (Other academic)
  • 475.
    Hollfelder, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Russel, Thembi
    Erasmus, Johannes Christoff
    Greeff, Jaco M
    Schlebusch, Carina Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Genetic patterns of sex-biased admixture in southern African populationsManuscript (preprint) (Other academic)
  • 476.
    Hollfelder, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Schlebusch, Carina M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Babiker, Hiba
    Dept. of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany..
    Hassan, Hisham Y.
    Banoon ART and Cytogenetics Centre, Bahrain Defense Force Hospital, Manama, Kingdom of Bahrain..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations2017In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, no 8, article id e1006976Article in journal (Refereed)
    Abstract [en]

    Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gateway out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping similar to 3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400-200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.

  • 477.
    Holmborn, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Habicher, Judith
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kasza, Zsolt
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Eriksson, Anna S.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Gorniok, Beata Filipek
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Gopal, Sandeep
    Couchman, John R.
    Ahlberg, Per Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wiweger, Malgorzata
    Spillmann, Dorothe
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kreuger, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ledin, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    On the Roles and Regulation of Chondroitin Sulfate and Heparan Sulfate in Zebrafish Pharyngeal Cartilage Morphogenesis2012In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 287, no 40, p. 33905-33916Article in journal (Refereed)
    Abstract [en]

    The present study addresses the roles of heparan sulfate (HS) proteoglycans and chondroitin sulfate (CS) proteoglycans in the development of zebrafish pharyngeal cartilage structures. uxs1 and b3gat3 mutants, predicted to have impaired biosynthesis of both HS and CS because of defective formation of the common proteoglycan linkage tetrasaccharide were analyzed along with ext2 and extl3 mutants, predicted to have defective HS polymerization. Notably, the effects on HS and CS biosynthesis in the respective mutant strains were shown to differ from what had been hypothesized. In uxs1 and b3gat3 mutant larvae, biosynthesis of CS was shown to be virtually abolished, whereas these mutants still were capable of synthesizing 50% of the HS produced in control larvae. extl3 and ext2 mutants on the other hand were shown to synthesize reduced amounts of hypersulfated HS. Further, extl3 mutants produced higher levels of CS than control larvae, whereas morpholino-mediated suppression of csgalnact1/csgalnact2 resulted in increased HS biosynthesis. Thus, the balance of the Extl3 and Csgalnact1/Csgalnact2 proteins influences the HS/CS ratio. A characterization of the pharyngeal cartilage element morphologies in the single mutant strains, as well as in ext2;uxs1 double mutants, was conducted. A correlation between HS and CS production and phenotypes was found, such that impaired HS biosynthesis was shown to affect chondrocyte intercalation, whereas impaired CS biosynthesis inhibited formation of the extracellular matrix surrounding chondrocytes.

  • 478. Hooge, Matthew
    et al.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Todt, Christiane
    Maloy, Aaron
    Jondelius, Ulf
    Tyler, Seth
    A revision of the systematics of panther worms (Hofstenia spp., Acoela), with notes on color variation and genetic variation within the genus2007In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 592, p. 439-454Article in journal (Refereed)
    Abstract [en]

    Species of the genus Hofstenia are voracious predators and among the largest and most colorful of the Acoela. They are known from Japan, the Red Sea, the North Atlantic islands of Bermuda and the Bahamas, and the Caribbean and in a variety of habitats including the rocky intertidal, among Thalassia sea grass, on filamentous algae and decaying mangrove leaves. Certain color morphs associated with each of these habitats seem to have confused the taxonomy of the group. While brown-and-white banding and spotting patterns of Hofstenia miamia and Hofstenia giselae are distinctive for species associated with mangrove leaves and Thallasia sp. and are likely to be cryptic for these specific environments, we find some evidence to suggest that the coloration is mimicry of a nudibranch with aposematic coloration. The common plan in these patterns is one with three variously solid or spotted lighter cross bands on a dark background. Our examination of museum type material and live specimens of Hofstenia collected from Bahamas, Belize, Bermuda, and Panama revealed no internal morphological differences between the Hofstenia species occurring in the Caribbean. Similarly, our analyses of 18S and 28S molecular sequence data revealed no significant differences among specimens. Accordingly, we declare that Hofstenia giselae is a junior synonym of Hofstenia miamia, the three- banded panther worm.

  • 479.
    Hosken, David J.
    et al.
    Univ Exeter, Ctr Ecol & Conservat, Penryn TR109EZ, Cornwall, England.
    Archer, C. Ruth
    Univ Exeter, Ctr Ecol & Conservat, Penryn TR109EZ, Cornwall, England.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England;Univ British Columbia, Dept Zool, Vancouver, BC V6T 1Z4, Canada.
    Sexual conflict2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 11, p. R451-R455Article, review/survey (Refereed)
  • 480.
    Hu, Yu-Zhi
    et al.
    Australian Natl Univ, Res Sch Earth Sci, Bldg 142 Mills Rd, Canberra, ACT 2601, Australia;Australian Natl Univ, Res Sch Phys & Engn, Bldg 60, Canberra, ACT 2601, Australia.
    Young, G. C.
    Australian Natl Univ, Res Sch Phys & Engn, Bldg 60, Canberra, ACT 2601, Australia.
    Burrow, Carole
    Queensland Museum, Geosci, 122 Gerler Rd, Hendra, Qld 4011, Australia.
    Zhu, You-an
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing 100044, Peoples R China.
    Lu, Jing
    Australian Natl Univ, Res Sch Phys & Engn, Bldg 60, Canberra, ACT 2601, Australia;Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing 100044, Peoples R China;CAS Ctr Excellence Life & Paleoenvironm, Beijing 100044, Peoples R China.
    High resolution XCT scanning reveals complex morphology of gnathal elements in an Early Devonian arthrodire2019In: PALAEOWORLD, ISSN 1871-174X, Vol. 28, no 4, p. 525-534Article in journal (Refereed)
    Abstract [en]

    Arthodire placoderms, as a possible sister group of Chinese 'maxillate' placoderms plus crown gnathostomes, provide important information regarding early evolution of jaws and teeth. High-resolution computed tomography and digital dissection on a unique articulated 400 million-year-old buchanosteid arthrodire permitsa detailed description of the three types of gnathal elements in basal arthrodires for the first time, giving insights into their morphology and the organization of the associated dentition. In displaying numerous denticle rows (dental fields), the gnathal element morphology is very different from the much-reduced denticulation of higher brachythoracid arthrodires, even though the latter have been used recently to interpret origin and early evolution of teeth. Ossification centres are anterolateral on the anterior supragnathal (attached to the braincase), anteromesial on the posterior supragnathal (attached to the palatoquadrate), and in the central part of the biting portion of the infragnathal (attached to the meckelian cartilage). The latter bone shows no evidence of two ossification centres as has been interpreted for more advanced arthrodires. Denticle rows radiating from the ossification centre form dental fields in all three elements, and are more similar to the gnathal elements of phlyctaeniid and actinolepid arthrodires than to advanced brachythoracids. The new evidence gives insights into the primitive arthrodire condition for comparison with the dermal jaw bones of Chinese 'maxillate' placoderms that have been homologised with the premaxilla, maxilla, and dentary of osteichthyans. The new details will help clarify the sequence of character acquisition in the evolution of marginal jaw bones in basal gnathostome groups.

  • 481.
    Hua, Wenjing
    et al.
    McMaster Univ, Dept Biol, Hamilton, ON L8S 4K1, Canada.
    Vogan, Aaron A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. McMaster Univ, Dept Biol, Hamilton, ON L8S 4K1, Canada.
    Xu, Jianping
    McMaster Univ, Dept Biol, Hamilton, ON L8S 4K1, Canada.
    Genotypic and Phenotypic Analyses of Two "Isogenic" Strains of the Human Fungal Pathogen Cryptococcus neoformans var. neoformans2019In: Mycopathologia, ISSN 0301-486X, E-ISSN 1573-0832, Vol. 184, no 2, p. 195-212Article in journal (Refereed)
    Abstract [en]

    The Cryptococcus neoformans species complex is a model organism for fungal studies. Many studies have used two strains, JEC20 and JEC21, and their derivatives. These two strains were obtained through 10 rounds of backcrosses and have been assumed near identical except at the mating-type locus. Here we obtained and compared the JEC20 genome sequence with the published JEC21 genome. Our comparison revealed 5322 single nucleotide polymorphisms (SNPs) with the majority (N=3816, 71.7%) located in three genomic regions, including the previously noted mating-type region. The remaining 1506 SNPs (28.3%) were distributed throughout all 14 chromosomes, predominantly at chromosomal ends. To study the potential effects of these three SNP-rich regions on phenotypes, 24 progenies from the JEC20xJEC21 cross representing eight recombinant genotypes were analyzed for their mating ability, melanin production, capsule formation, and growths at 30 degrees C and 40 degrees C. Significant phenotypic variations were found among the progeny. However, the observed phenotypic variations could not be explained by the three SNP-rich regions. Further genome sequencing of our JEC21 and the 24 progenies revealed only six segregating SNPs outside of the three SNP-rich regions between JEC20 and JEC21, a result indicating that the 1500 SNPs identified in the published JEC21 genome might be caused by sequencing errors and/or strain mixing. However, the six SNPs and the three SNP-rich regions could not explain the observed phenotypic variations. Our analyses suggest that spontaneous mutations accumulated under laboratory conditions could have significant effects on phenotypes and on our interpretations of experimental results.

  • 482.
    Hussein, Juma
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tibuhwa, Donatha Damian
    University of Dar es Salaam, Department of molecular Biology and Biotechnology.
    Tibell, Sanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Phylogenetic position and taxonomy of Kusaghiporia usambarensis gen. et sp. nov. (Polyporales)2018In: Mycology, ISSN 2150-1203Article in journal (Refereed)
    Abstract [en]

    A large polyporoid mushroom from the West Usambara Mountains in North-eastern Tanzania produces dark brown, up to 60-cm large fruiting bodies that at maturity may weigh more than 10 kg. It has a high rate of mycelial growth and regeneration and was found growing on both dry and green leaves of shrubs; attached to the base of living trees, and it was also observed to degrade dead snakes and insects accidentally coming into contact with it. Phylogenetic analyses based on individual and concatenated data sets of nrLSU, nrSSU and the RPB2 and TEF1 genes showed it, together with Laetiporus, Phaeolus, Pycnoporellus and Wolfiporia, to form a monophyletic group in Polyporales. Based on morphological features and molecular data, it is described as Kusaghiporia usambarensis.

  • 483. Hyde, Kevin D
    et al.
    Udayanga, Dhanushka
    Manamgoda, Dimuthu S
    Tedersoo, Leho
    Larsson, Ellen
    Göteborgs Universitet.
    Abarenkov, Kessy
    Bertrand, Yann JK
    Göteborgs Universitet.
    Oxelman, Bengt
    Göteborgs Universitet.
    Hartmann, Martin
    Kauserud, Håvard
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kristiansson, Erik
    Nilsson, R. Henrik
    Göteborgs Universitet.
    Incorporating molecular data in fungal systematics: a guide for aspiring researchers2013In: Current Research in Environmental & Applied Mycology, ISSN 2229-2225, Vol. 3, no 1, p. 1-32Article in journal (Refereed)
  • 484.
    Ickert-Bond, Stephanie M.
    et al.
    University of Alaska, Fairbanks.
    Rydin, Catarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Micromorphology of the seed envelope of Ephedra L. (Gnetales) and its relevance for the timing of evolutionary events2011In: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 172, no 1, p. 36-48Article in journal (Refereed)
    Abstract [en]

    Micromorphology of the seed envelope of Ephedra (Gnetales) is known to be variable, but variation patternshave never been systematically documented. We test the usefulness of this feature for species determination and subclade delimitation in Ephedra and investigate the relationship of this character to infrageneric evolutionarypatterns. Most species have a basically smooth seed envelope, which in some species appears slightly striate or reticulate due to convex or depressed outer periclinal cell walls. Ephedra rhytidosperma from China and Ephedra torreyana from North America have transverse lamellae formed by the epidermis. A papillate surfaceis found in respective close relatives of these two species. Micromorphology of the seed envelope is generally not useful for species identification or subclade delineation. The amount of variation is low, and intraspecific variation, which in some cases seems to be correlated with hybridization and/or introgression, complicates species recognition. Furthermore, parallel evolution of similar micromorphological patterns in unrelated subclades of Ephedra is evident and cannot be explained by similar seed dispersal mechanisms. The Asian species with transverse lamellae or papillae on the seed are dispersed by frugivores whereas similar American species are anemochoric. Transverse ridges occur in several Early Cretaceous fossil seeds with affinity to Ephedra. However, our results indicate that the resemblance between these fossils and extant taxa with similar features is superficial and convergent. In line with other recent studies, we find that Cretaceous ephedroids are extinct stem relatives to the extant clade.

  • 485.
    Idnurm, Alexander
    et al.
    Univ Melbourne, Sch Biosci, Melbourne, Vic 3010, Australia..
    Hood, Michael E.
    Amherst Coll, Dept Biol, Amherst, MA 01002 USA..
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Giraud, Tatiana
    Univ Paris 11, Lab Ecol Systemat & Evolut, UMR 8079, F-91405 Orsay, France.;CNRS, F-91405 Orsay, France..
    Contrasted patterns in mating-type chromosomes in fungi: Hotspots versus coldspots of recombination2015In: Mycologist, ISSN 1749-4613, E-ISSN 1878-0253, Vol. 29, no 3-4, p. 220-229Article, review/survey (Refereed)
    Abstract [en]

    It is striking that, while central to sexual reproduction, the genomic regions determining sex or mating-types are often characterized by suppressed recombination that leads to a decrease in the efficiency of selection, shelters genetic load, and inevitably contributes to their genic degeneration. Research on model and lesser-explored fungi has revealed similarities in recombination suppression of the genomic regions involved in mating compatibility across eukaryotes, but fungi also provide opposite examples of enhanced recombination in the genomic regions that determine their mating types. These contrasted patterns of genetic recombination (sensu lato, including gene conversion and ectopic recombination) in regions of the genome involved in mating compatibility point to important yet complex processes occurring in their evolution. A number of pieces in this puzzle remain to be solved, in particular on the unclear selective forces that may cause the patterns of recombination, prompting theoretical developments and experimental studies. This review thus points to fungi as a fascinating group for studying the various evolutionary forces at play in the genomic regions involved in mating compatibility.

  • 486.
    Irisarri, Iker
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Konstanz, Dept Biol, Lehrstuhl Zool & Evolut Biol, Univ Str 10, D-78464 Constance, Germany.
    Baurain, Denis
    Univ Liege, InBioS Eukaryot Phylogen, Dept Life Sci & PhytoSYST, B-4000 Liege, Belgium.
    Brinkmann, Henner
    Leibniz Inst DSMZ German Collect Microorgan & Cell, D-38124 Braunschweig, Germany.
    Delsuc, Frédéric
    Univ Montpellier, Inst Sci Evolut, UMR 5554, CNRS,IRD,EPHE, F-34095 Montpellier, France.
    Sire, Jean-Yves
    Sorbonne Univ, Inst Biol Paris Seine, UMR7138, F-75005 Paris, France.
    Kupfer, Alexander
    Stuttgart State Museum Nat Hist, Dept Zool, D-70191 Stuttgart, Germany.
    Petersen, Jörn
    Leibniz Inst DSMZ German Collect Microorgan & Cell, D-38124 Braunschweig, Germany.
    Jarek, Michael
    Helmholtz Ctr Infect Res, Dept Genome Analyt, D-38124 Braunschweig, Germany.
    Meyer, Axel
    Univ Konstanz, Dept Biol, Lehrstuhl Zool & Evolut Biol, Univ Str 10, D-78464 Constance, Germany.
    Vences, Miguel
    Braunschweig Univ Technol, Zool Inst, D-38106 Braunschweig, Germany.
    Philippe, Hervé
    Ctr Biodivers Theory & Modelling, UMR CNRS 5321, Stn Theoret & Expt Ecol, F-09200 Moulis, France; Univ Montreal, Dept Biochim, Montreal, PQ H3C 3J7, Canada.
    Phylotranscriptomic consolidation of the jawed vertebrate timetree2017In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 1, no 9, p. 1370-1378Article in journal (Refereed)
    Abstract [en]

    Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on ‘standards’ for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as a model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial. We tested a new bioinformatic pipeline to assemble large and accu- rate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost- effective. Increased sequencing effort up to about 10 Gbp allows more genes to be recovered, but shallower sequencing (1.5 Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.

  • 487.
    Irwin, Nicholas
    et al.
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Tikhonenkov, Denis
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada;Russian Acad Sci, Inst Biol Inland Waters, Borok 152742, Russia.
    Hehenberger, Elisabeth
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada;Monterey Bay Aquarium Res Inst, Moss Landing, CA USA.
    Mylnikov, Alexander
    Russian Acad Sci, Inst Biol Inland Waters, Borok 152742, Russia.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Keeling, Patrick
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Phylogenomics supports the monophyly of the Cercozoa2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 130, p. 416-423Article in journal (Refereed)
    Abstract [en]

    The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, including phylogenomic approaches, have produced ambiguous results and raised doubts about the monophyly of the group. Here we sought to resolve these ambiguities using a 161-gene phylogenetic dataset with data from newly available genomes and deeply sequenced transcriptomes, including three new transcriptomes from Aurigamonas soils, Abollifer prolabens, and a novel species, Lapot gusevi n. gen. n. sp. Our phylogenomic analysis strongly supported a monophyletic Cercozoa, and approximately-unbiased tests rejected the paraphyletic topologies observed in previous studies. The transcriptome of L. gusevi represents the first transcriptomic data from the large and recently characterized Aquavolonidae-Treumulida-'Novel Clade 12' group, and phylogenomics supported i