Latest update: Oct 2019


Johan Nylander - Download page

Johan


Contact

@: Johan.Nylander-at-abc-dot-se


Programs/Scripts/Code

Note: All code are now on my GitHub page: https://github.com/nylander


Links to software on other pages

Note: Most of the code is now migrated to my pages on GitHub


Text

Note: A publication list can be found on my Google Scholar page. PDFs and Supplementary information, etc, can still be found here.

  1. [PDF] Elmquist, K., et al. 1995.
    Black Lizards: Melanistic morph of the Common lizard (Lacerta vivipara).
    Memoranda Societas pro Fauna et Flora Fennica 71:144-145.

  2. [PDF] Nylander, J.A.A., et al. 1999.
    A test of monophyly of the gutless Phallodrilinae (Oligochaeta, Tubificidae) and the use of a 573 bp region of the mitochondrial cytochrome oxidase I gene in analysis of annelid phylogeny.
    Zoologica Scripta 28:305-313.

  3. [PDF] Nylander, J.A.A. 2001.
    Taxonomic sampling in phylogenetic analysis: Problems and strategies reviewed.
    Research Essay No. 1. Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University.

  4. [PDF|Suppl.] Rokas, A., et al. 2002.
    A maximum likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae); implications for insect phylogenetic studies.
    Molecular Phylogenetics and Evolution 22:206-219.

  5. [PDF|Code] Nylander, J.A.A., et al. 2004.
    Bayesian phylogenetic analysis of combined data.
    Systematic Biology 53:47-67.

  6. [PDF] Nylander, J.A.A. 2004.
    Bayesian phylogenetics and the evolution of gall wasps.
    Summaries of Uppsala Dissertations from the Faculty of Science and Technology ISSN 1104-232X; 937.

  7. [PDF|Suppl.] Irestedt, M., et al. 2004.
    Phylogenetic relationships of typical Antbirds (Thamnophilidae) and test of incongruence based on Bayes factors.
    BMC Evolutionary Biology 4:23.

  8. [PDF] Beier, B.-A., et al. 2004.
    Phylogenetic relationships and biography of the desert plant genus Fagonia (Zygophyllaceae), inferred by parsimony and Bayesian model averaging.
    Molecular Phylogenetics and Evolution 33:91-108.

  9. [PDF|Suppl.] Buffington, M.L., et al. 2007.
    The phylogeny and evolution of Figitidae (Hymenoptera: Cynipoidea).
    Cladistics 23:403-431.

  10. [PDF] Buffington, M.L., et al. 2007.
    The phylogeny and evolution of Figitidae (Hymenoptera: Cynipoidea).
    Cladistics 23:403-431.

  11. [PDF|AWTY Online.] Nylander, J.A.A., et al. 2008.
    AWTY (Are We There Yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics.
    Bioinformatics 24:581-583.

  12. [PDF|Code.] Nylander, J.A.A., et al. 2008.
    Accounting for phylogenetic uncertainty in biogeography: A Bayesian approach to dispersal- vicariance analysis of the thrushes (Aves: Turdus).
    Systematic Biology 57:257-268.

  13. [PDF] Buerki, S., et al. 2009.
    Plastid and nuclear DNA markers reveal intricate relationships at subfamilial and tribal levels in the soapberry family (Sapindaceae).
    Molecular Phylogenetics and Evolution 51:238-258.

  14. [PDF] Lundberg, M., et al. 2009.
    Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification.
    Molecular Phylogenetics and Evolution 51:269-280.

  15. [PDF|Suppl.] Antonelli, A., et al. 2009.
    Tracing the impact of the Andean uplift on Neotropical plant evolution: evidence from the coffee family.
    Proceedings of the National Academy of Sciences 106:9749-9754.

  16. [PDF] Nieves-Aldrey, J.-L., et al. 2009.
    Revision and phylogenetics of the genus Paraulax Kieffer (Hymenoptera, Cynipidae) with biological notes and description of a new tribe, a new genus, and five new species.
    Zootaxa 2200:1-40.

  17. [PDF|Suppl.] Buckley, L., et al. 2009.
    The phylogenetic placement and biogeographical origins of the New Zealand stick insects (Phasmatodea).
    Systematic Entomolgy 35:205-225.

  18. [PDF|Suppl.] Ran, L., et al. 2010.
    Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium.
    PLoS One 5:e11486.

  19. [PDF|Suppl.] Jønsson, K.A., et al. 2010.
    Biogeographical history of cuckoo-shrikes (Aves: Passeriformes): transoceanic colonization of Africa from Australo-Papua.
    Journal of Biogeography 37:1767-1781.

  20. [PDF|Suppl.] Buerki, S., et al. 2011.
    An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the worldwide plant soapberry family (Sapindaceae).
    Journal of Biogeography 38:531-550.

  21. [PDF|Suppl.] Larsson, J., et al. 2011.
    Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits.
    BMC Evolutionary Biology 11:187.

  22. [PDF|Suppl.] Nilsson, R.H., et al. 2012.
    Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences.
    MycoKeys 4:37-63.

  23. [PDF|Suppl.] Ericson, P.G.P., et al. 2014.
    Dating the diversification of the major lineages of Passeriformes (Aves).
    BMC Evolutionary Biology 14:8.

  24. [PDF|Suppl.] Dupont, C.L., et al. 2014.
    Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition.
    PLoS One 9:e89549.

  25. [PDF|Suppl.] Vigil-Stenman, T., et al. 2015.
    Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.
    BMC Genomics 16:193.

  26. [PDF|Suppl.] Ronquist, F., et al. 2015.
    Phylogeny, Evolution and Classification of Gall Wasps: The Plot Thickens.
    PLoS One 10(5):e0123301.

  27. [PDF|Suppl.] Mendoza, L., et al. 2016.
    Metagenomic analysis from the interior of a speleothem in Tjuv-Ante's Cave, Northern Sweden.
    PLoS One 11(3):e0155757.

  28. [PDF|Suppl.] Díez, B., et al. 2016.
    Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.
    PLoS One 11(5):e0155757

  29. [PDF|Suppl.] Lilja, T., et al. 2017.
    Species identification of Swedish mosquitoes through DNA metabarcoding.
    Journal of the European Mosquito Control Association 35:1-9.

  30. [PDF|Suppl.] Dalén, L., et al. 2017.
    Identifying bird remains using ancient DNA barcoding.
    Genes 8:169.

  31. [PDF] Swenson, U., et al. 2018.
    Phylogeny, species delimitation and revision of Pleioluma (Sapotaceae) in New Caledonia, a frequently gynodioecious genus.
    Australian Systematic Botany 31:120-165.

  32. [PDF] Ronquist, F., et al. 2018.
    Life history of Parnips and the evolutionary origin of gall wasps.
    Journal of Hymenoptera Research 65:91-110.

  33. [PDF|Suppl.] Caputo, A., et al. 2019.
    The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration.
    FEMS microbiology letters 366 (2), fny297.

  34. [PDF|Suppl.] Prost, A., et al. 2019.
    Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.
    GigaScience 8 (5), giz003.


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