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  • 1.
    Caputo, A
    et al.
    Stockholm University.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    Foster, R A
    Stockholm University.
    The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration2019In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 366, no 2, article id fny297Article in journal (Refereed)
  • 2.
    Dalen, Love
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lagerholm, Vendela K.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nylander, Johan A. A.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Barton, Nick
    Bochenski, Zbigniew M.
    Tomek, Teresa
    Rudling, David
    Ericson, Per G. P.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Stewart, John R.
    Identifying Bird Remains Using Ancient DNA Barcoding2017In: Genes, E-ISSN 2073-4425, Vol. 8, no 6, article id 169Article in journal (Refereed)
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  • 3. Dupont, Chris L
    et al.
    Larsson, John
    Yooseph, Shibu
    Ininbergs, Karolina
    Goll, Johannes
    Asplund-Samuelsson, Johannes
    McCrow, John P
    Celepli, Narin
    Allen, Lisa Zeigler
    Ekman, Martin
    Lucas, Andrew J
    Hagström, Åke
    Thiagarajan, Mathangi
    Brindefalk, Björn
    Richter, Alexander R
    Andersson, Anders F
    Tenney, Aaron
    Lundin, Daniel
    Tovchigrechko, Andrey
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Brami, Daniel
    Badger, Jonathan H
    Allen, Andrew E
    Rusch, Douglas B
    Hoffman, Jeff
    Norrby, Erling
    Friedman, Robert
    Pinhassi, Jarone
    Venter, J Craig
    Bergman, Birgitta
    Functional tradeoffs underpin salinity-driven divergence in microbial community composition.2014In: PloS one, ISSN 1932-6203, Vol. 9, no 2, p. e89549-Article in journal (Refereed)
    Abstract [en]

    Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

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  • 4. Díez, Beatriz
    et al.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. BILS.
    Ininbergs, Karolina
    Dupont, Christopher L
    Allen, Andrew E
    Yooseph, Shibu
    Rusch, Douglas B
    Bergman, Birgitta
    Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.2016In: PLOS ONE, E-ISSN 1932-6203, Vol. 11, no 5Article in journal (Refereed)
    Abstract [en]

    Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.

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  • 5.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nylander, Johan A A
    Christidis, Les
    Joseph, Leo
    Qu, Yanhua
    Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics2020In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 69, no 5, p. 820-829Article in journal (Refereed)
    Abstract [en]

    The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits.

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  • 6.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Klopfstein, Seraina
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nguyen, Jacqueline MT
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dating the diversification of the major lineages of Passeriformes (Aves)2014In: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 14, no 8, p. 1-15Article in journal (Refereed)
    Abstract [en]

    Background: The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% ofall living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the lateCretaceous. However, previous molecular dating studies have relied heavily on the geological split between NewZealand and Antarctica, assumed to have occurred 85–82 Mya, for calibrating the molecular clock and might thusbe circular in their argument.Results: This study provides a time-scale for the evolution of the major clades of passerines using seven nuclearmarkers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealandsplit from Antarctica 85–52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretationsof the New Zealand–Antarctica vicariance event influence our age estimates. Our results suggest that thediversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration forthe New Zealand–Antarctica vicariance event (85–52 Mya) dramatically increases the 95% credibility intervals andleads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genesanalyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines,which can be used as secondary calibration points in future molecular studies.Conclusions: Our analysis takes recent paleontological and geological findings into account and provides the bestestimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporalframework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, andadds to the growing support for a Cretaceous origin of Passeriformes.

  • 7.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Phylogenetic relationships of typical antbirds (Thamnophilidae) and test of incongruence based on Bayes factors.2004In: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 4, p. 23-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The typical antbirds (Thamnophilidae) form a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly understood. Herein, we present a hypothesis of the generic relationships of this group based on Bayesian inference analyses of two nuclear introns and the mitochondrial cytochrome b gene. The level of phylogenetic congruence between the individual genes has been investigated utilizing Bayes factors. We also explore how changes in the substitution models affected the observed incongruence between partitions of our data set.

    RESULTS: The phylogenetic analysis supports both novel relationships, as well as traditional groupings. Among the more interesting novel relationship suggested is that the Terenura antwrens, the wing-banded antbird (Myrmornis torquata), the spot-winged antshrike (Pygiptila stellaris) and the russet antshrike (Thamnistes anabatinus) are sisters to all other typical antbirds. The remaining genera fall into two major clades. The first includes antshrikes, antvireos and the Herpsilochmus antwrens, while the second clade consists of most antwren genera, the Myrmeciza antbirds, the "professional" ant-following antbirds, and allied species. Our results also support previously suggested polyphyly of Myrmotherula antwrens and Myrmeciza antbirds. The tests of phylogenetic incongruence, using Bayes factors, clearly suggests that allowing the gene partitions to have separate topology parameters clearly increased the model likelihood. However, changing a component of the nucleotide substitution model had much higher impact on the model likelihood.

    CONCLUSIONS: The phylogenetic results are in broad agreement with traditional classification of the typical antbirds, but some relationships are unexpected based on external morphology. In these cases their true affinities may have been obscured by convergent evolution and morphological adaptations to new habitats or food sources, and genera like Myrmeciza antbirds and the Myrmotherula antwrens obviously need taxonomic revisions. Although, Bayes factors seem promising for evaluating the relative contribution of components to an evolutionary model, the results suggests that even if strong evidence for a model allowing separate topology parameters is found, this might not mean strong evidence for separate gene phylogenies, as long as vital components of the substitution model are still missing.

  • 8.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Johansson, Frank
    Thörn, Filip
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    Azurmes, surmes eller mitt emellan: Vi har ett resultat2022In: Roadrunner, ISSN 1402-2451, Vol. 30, no 3-4, p. 38-44Article in journal (Other (popular science, discussion, etc.))
  • 9.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Thörn, Filip
    Ericson, Per G.P.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    van Grouw, Hein
    Red'kin, Yaroslav A.
    Hellquist, Alexander
    Johansson, Frank
    Nylander, Johan A.A.
    A crowd-sourced genomic project to assess hybrid content in a rare avian vagrant (Azure Tit Cyanistes cyanus (Pallas, 1770))2023In: Avian Research, ISSN 2053-7166, Vol. 14, p. 100130-100130, article id 100130Article in journal (Refereed)
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  • 10.
    Lilja, Tobias
    et al.
    SVA, National Veterinary Institute.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    Troell, Karin
    SVA, National Veterinary Institute.
    Lindström, Anders
    SVA, National Veterinary Institute.
    Species identification of Swedish mosquitoes through DNA metabarcoding2017In: Journal of the European Mosquito Control Association, Vol. 35, p. 1-9Article in journal (Refereed)
    Abstract [en]

    DNA-barcoding utilises a fragment of the mitochondrial cytochrome oxidase subunit 1 (COI) gene to identify most animal species. Using next generation sequencing (NGS), this method can be further developed into metabarcoding processes that allow the simultaneous identification of several species from a mixed sample. We created a database of COI sequences of 27 mosquito species collected in Sweden, and combined our data with 27 additional sequences from GenBank to cover the taxa recently documented in Sweden and to include possible invasive taxa. Comparisons show that COI metabarcoding reliably identifies 41 of 54 species and the remainder to species group. Using three independent primer pairs along the COI gene, we further developed this barcoding approach to simultaneously identify Swedish mosquitoes in communities using NGS and quantify relative abundance of each mosquito species in the sample, using bioinformatics methods. We tested the accuracy of the metabarcoding method using communities assembled from morphologically identified mosquitoes, revealing 80% positive identification rate and the estimates of population structure which reflects the input sample. We conclude that metabarcoding is useful as a high throughput identification technique and for the quantification of species.

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    JEMCA 35 p 1-9 Supplementary Material_p1-8.pdf
  • 11.
    Lähteenaro, Meri
    et al.
    Swedish Museum of Natural History, Department of Zoology. Department of Zoology Swedish Museum of Natural History Stockholm Sweden;Department of Zoology, Faculty of Science Stockholm University Stockholm Sweden.
    Straka, Jakub
    Department of Zoology, Faculty of Science Charles University Prague Czech Republic.
    Forshage, Mattias
    Swedish Museum of Natural History, Department of Zoology. Department of Zoology Swedish Museum of Natural History Stockholm Sweden.
    Hovmöller, Rasmus
    Department of Zoology Swedish Museum of Natural History Stockholm Sweden;SLU Swedish Species Information Centre Uppsala Sweden.
    Nakase, Yuta
    Faculty of the Arts Kyoto University of the Arts Kyoto Japan.
    Nilsson, Anders L.
    Museum of Evolution, Uppsala University Uppsala Sweden.
    Smit, John T.
    Naturalis Biodiversity Center Leiden The Netherlands;European Invertebrate Survey Leiden The Netherlands.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    Bergsten, Johannes
    Swedish Museum of Natural History, Department of Zoology. Department of Zoology Swedish Museum of Natural History Stockholm Sweden;Department of Zoology, Faculty of Science Stockholm University Stockholm Sweden.
    Phylogenomic species delimitation of the twisted‐winged parasite genus Stylops (Strepsiptera)2023In: Systematic Entomology, ISSN 0307-6970, E-ISSN 1365-3113Article in journal (Refereed)
  • 12.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    En resa till Iran - huggormarnas land: Del 1. Drömmen om Latifis huggorm2022In: Snoken, ISSN 0347-7630, Vol. 51, no 2, p. 20-27Article in journal (Other (popular science, discussion, etc.))
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  • 13.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    Ett fynd av leucistisk snok: En mycket ovanlig genvariant2022In: Snoken, ISSN 0347-7630, Vol. 51, no 2, p. 4-7Article in journal (Other (popular science, discussion, etc.))
    Abstract [en]

    An observation of a female leucistic Grass snake (Natrix natrix (L.)), found in Kungsängen, Uppland, Sweden on August 26, 2022, is discussed. The observation is the first for Sweden and possibly the first for the species.

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  • 14.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    Fynd av svarta och vita ormar i Sverige2022In: Fauna & flora: en spegling av svensk natur, E-ISSN 0014-8903, Vol. 117, no 4, p. 2-8Article in journal (Other (popular science, discussion, etc.))
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  • 15. Prost, Stefan
    et al.
    Armstrong, Ellie E.
    Nylander, Johan
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Thomas, Gregg W. C.
    Suh, Alexander
    Petersen, Bent
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Benz, Brett W.
    Blom, Mozes P. K.
    Palkopoulou, Eleftheria
    Ericson, Per G. P.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise2019In: GigaScience, E-ISSN 2047-217X, Vol. 8, no 5Article in journal (Refereed)
    Abstract [en]

    The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and nonscientists alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group’s extensive phenotypic diversity. We found genes important for coloration, morphology, and feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found Gene Ontology categories for “startle response” and “olfactory receptor activity” to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.

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  • 16. Reeve, Andrew Hart
    et al.
    Kennedy, Jonathan David
    Pujolar, José Martín
    Petersen, Bent
    Blom, Mozes P. K.
    Alström, Per
    Haryoko, Tri
    Ericson, Per G. P.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Naturhistoriska riksmuseet.
    Nylander, Johan A. A.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jønsson, Knud Andreas
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    The formation of the Indo-Pacific montane avifauna2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 8215Article in journal (Refereed)
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  • 17.
    Ronquist, Fredrik
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nieves-Aldrey, José-Luis
    Buffington, Matthew L
    Liu, Zhiwei
    Liljeblad, Johan
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. BILS.
    Phylogeny, evolution and classification of gall wasps: the plot thickens.2015In: PLOS ONE, E-ISSN 1932-6203, Vol. 10, no 5Article in journal (Refereed)
    Abstract [en]

    Gall wasps (Cynipidae) represent the most spectacular radiation of gall-inducing insects. In addition to true gall formers, gall wasps also include phytophagous inquilines, which live inside the galls induced by gall wasps or other insects. Here we present the first comprehensive molecular and total-evidence analyses of higher-level gall wasp relationships. We studied more than 100 taxa representing a rich selection of outgroups and the majority of described cynipid genera outside the diverse oak gall wasps (Cynipini), which were more sparsely sampled. About 5 kb of nucleotide data from one mitochondrial (COI) and four nuclear (28S, LWRh, EF1alpha F1, and EF1alpha F2) markers were analyzed separately and in combination with morphological and life-history data. According to previous morphology-based studies, gall wasps evolved in the Northern Hemisphere and were initially herb gallers. Inquilines originated once from gall inducers that lost the ability to initiate galls. Our results, albeit not conclusive, suggest a different scenario. The first gall wasps were more likely associated with woody host plants, and there must have been multiple origins of gall inducers, inquilines or both. One possibility is that gall inducers arose independently from inquilines in several lineages. Except for these surprising results, our analyses are largely consistent with previous studies. They confirm that gall wasps are conservative in their host-plant preferences, and that herb-galling lineages have radiated repeatedly onto the same set of unrelated host plants. We propose a revised classification of the family into twelve tribes, which are strongly supported as monophyletic across independent datasets. Four are new: Aulacideini, Phanacidini, Diastrophini and Ceroptresini. We present a key to the tribes and discuss their morphological and biological diversity. Until the relationships among the tribes are resolved, the origin and early evolution of gall wasps will remain elusive.

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  • 18.
    Ronquist, Fredrik
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nylander, Johan
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Vårdal, Hege
    Swedish Museum of Natural History, Department of Zoology.
    Nieves-Aldrey, José Luis
    Life history of Parnips and the evolutionary origin of gall wasps2018In: Journal of Hymenoptera Research, ISSN 1070-9428, E-ISSN 1314-2607, Vol. 65, p. 91-110Article in journal (Refereed)
    Abstract [en]

    By mechanisms that are still unknown, gall wasps (Cynipidae) induce plants to form complex galls, inside which their larvae develop. The family also includes inquilines (phytophagous forms that live inside the galls of other gall inducers) and possibly also parasitoids of gall inducers. The origin of cynipids is shrouded in mystery, but it has been clear for some time that a key group in making progress on this question is the ‘figitoid inquilines’. They are gall-associated relatives of cynipids, whose biology is poorly known. Here, we report the first detailed data on the life history of a figitoid inquiline, the genus Parnips. Dissections of mature galls show that Parnips nigripes is a parasitoid of Barbotinia oraniensis, a cynipid that induces single-chambered galls inside the seed capsules of annual poppies (Papaver rhoeas and P. dubium). Galls with pupae of Parnips nigripes always contain the remains of a terminal-instar larva of B. oraniensis. The mandibles of the terminal-instar larva of P. nigripes are small and equipped with a single sharp tooth, a shape that is characteristic of carnivorous larvae. The weight of P. nigripes pupae closely match that of the same sex of B. oraniensis pupae, indicating that Parnips makes efficient use of its host and suggesting that ovipositing Parnips females lay eggs that match the sex of the host larva. Dissection of young galls show that another species of Parnips, hitherto undescribed, spends its late larval life as an ectoparasitoid of Iraella hispanica, a cynipid that induces galls in flowers of annual poppies. These and other observations suggest that Parnips shares the early endoparasitic-late ectoparasitic life history described for all other cynipoid parasitoids. Our findings imply that gall wasps evolved from parasitoids of gall insects. The original hosts could not have been cynipids but possibly chalcidoids, which appear to be the hosts of several extant figitoid inquilines. It is still unclear whether the gall inducers evolved rapidly from these ancestral parasitoids, or whether they were preceded by a long series of intermediate forms that were phytophagous inquilines.

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  • 19. Singh, Abhijeet
    et al.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    Schnürer, Anna
    Bongcam-Rudloff, Erik
    Müller, Bettina
    High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.2020In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 11, article id 2066Article in journal (Refereed)
    Abstract [en]

    The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline "AcetoScan" presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.

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  • 20. Vigil-Stenman, Theoden
    et al.
    Larsson, John
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. BILS.
    Bergman, Birgitta
    Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.2015In: BMC Genomics, E-ISSN 1471-2164, Vol. 16Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Insertion sequences (ISs) are approximately 1 kbp long "jumping" genes found in prokaryotes. ISs encode the protein Transposase, which facilitates the excision and reinsertion of ISs in genomes, making these sequences a type of class I ("cut-and-paste") Mobile Genetic Elements. ISs are proposed to be involved in the reductive evolution of symbiotic prokaryotes. Our previous sequencing of the genome of the cyanobacterium 'Nostoc azollae' 0708, living in a tight perpetual symbiotic association with a plant (the water fern Azolla), revealed the presence of an eroding genome, with a high number of insertion sequences (ISs) together with an unprecedented large proportion of pseudogenes. To investigate the role of ISs in the reductive evolution of 'Nostoc azollae' 0708, and potentially in the formation of pseudogenes, a bioinformatic investigation of the IS identities and positions in 47 cyanobacterial genomes was conducted. To widen the scope, the IS contents were analysed qualitatively and quantitatively in 20 other genomes representing both free-living and symbiotic bacteria.

    RESULTS: Insertion Sequences were not randomly distributed in the bacterial genomes and were found to transpose short distances from their original location ("local hopping") and pseudogenes were enriched in the vicinity of IS elements. In general, symbiotic organisms showed higher densities of IS elements and pseudogenes than non-symbiotic bacteria. A total of 1108 distinct repeated sequences over 500 bp were identified in the 67 genomes investigated. In the genome of 'Nostoc azollae' 0708, IS elements were apparent at 970 locations (14.3%), with 428 being full-length. Morphologically complex cyanobacteria with large genomes showed higher frequencies of IS elements, irrespective of life style.

    CONCLUSIONS: The apparent co-location of IS elements and pseudogenes found in prokaryotic genomes implies earlier IS transpositions into genes. As transpositions tend to be local rather than genome wide this likely explains the proximity between IS elements and pseudogenes. These findings suggest that ISs facilitate the reductive evolution in for instance in the symbiotic cyanobacterium 'Nostoc azollae' 0708 and in other obligate prokaryotic symbionts.

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  • 21.
    Zepeda Mendoza, Marie Lisandra
    et al.
    Natural History Museum of Denmark.
    Lundberg, Johannes
    Swedish Museum of Natural History, Department of Botany.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Department of Paleobiology. Nordic Center for Earth Evolution (NordCEE).
    Campos, Paula
    University of Copenhagen.
    Nylander, Johan A. A.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Sallstedt, Thereese
    Swedish Museum of Natural History, Department of Paleobiology. Nordic Center for Earth Evolution (NordCEE).
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden2016In: PLOS ONE, E-ISSN 1932-6203, Vol. 11, no 3, p. 1-23, article id e015177Article in journal (Refereed)
    Abstract [en]

    Speleothems are secondary mineral deposits normally formed by water supersaturated with calcium carbonate percolating into underground caves, and are often associated with low-nutrient and mostly non-phototrophic conditions. Tjuv-Ante’s cave is a shallow-depth cave formed by the action of waves, with granite and dolerite as major components, and opal-A and calcite as part of the speleothems, making it a rare kind of cave. We generated two DNA shotgun sequencing metagenomic datasets from the interior of a speleothem from Tjuv-Ante’s cave representing areas of old and relatively recent speleothem formation. We used these datasets to perform i) an evaluation of the use of these speleothems as past biodiversity archives, ii) functional and taxonomic profiling of the speleothem’s different formation periods, and iii) taxonomic comparison of the metagenomic results to previous microscopic analyses from a nearby speleothem of the same cave. Our analyses confirm the abundance of Actinobacteria and fungi as previously reported by microscopic analyses on this cave, however we also discovered a larger biodiversity. Interestingly, we identified photosynthetic genes, as well as genes related to iron and sulphur metabolism, suggesting the presence of chemoautotrophs. Furthermore, we identified taxa and functions related to biomineralization. However, we could not confidently establish the use of this type of speleothems as biological paleoarchives due to the potential leaching from the outside of the cave and the DNA damage that we propose has been caused by the fungal chemical etching.

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