111 research outputs found
Speciation research as well as career paths
No full textMartin Stervander delivered an invited presentation on speciation research as well as career paths to the Graduate Research School in Genomic Ecology (GENECO) final meeting in Höör, Swede
Diversification history and morphological evolution of larks
No full textEcomorphological and biogeographical data for all lark species included in the study.R code employed to conduct the analyses. Please, note that we did not incorporate in the manuscript all analyses explored in the R script; in some cases, we built similar models using different approaches and R packages (‘PANDA’, ‘DDD’, ‘laser’, ‘diversitree’) to test the consistency of our results. Thus, this is not an exhaustive set of code but serves to demonstrate the approaches employed in this study.Peer reviewe
Data associated with the publication "The origin of the world's smallest flightless bird, the Inaccessible Island Rail Atlantisia rogersi (Aves: Rallidae)"
No full textDESCRIPTION OF FILES
These are files including data and additional results, that support the paper "The origin of the world's smallest flightless bird, the Inaccessible Island Rail Atlantisia rogersi (Aves: Rallidae)", by Stervander et al. 2018, published in Molecular Phylogenetics and Evolution (doi: 10.1016/j.ympev.2018.10.007).
The phylogenetic analyses focus on rails (Aves: Rallidae) and outgroups based on (1) a dataset, 'MtProt' comprising the coding sequences (cds) from full mitochondrial genome assemblyes, and (2) a mixed-marker dataset, '2Nc3Mt', comprising the mitochondrial markers cytochrome b (cytb), cytochrome oxidase subunit I (COI), and 16S ribosomal RNA (16S), and the nuclear markers β-fibrinogen intron 7 (bFib7) and recombination activating gene 1 (RAG1). The latter dataset i largely based on data from Garcia-R et al. (2014), with additions of the Inaccessible Island Rail Atlantisia rogersi and some further sequences (see our paper).
Trees mentioned in our paper as "results not shown" can be found below.
This deposition contains five groups of data:
1. Beast input xml files for phylogenetic analyses
2. Beast output: log files
3. Beast output: raw tree files
4. Beast output: Maximum Clade Credibility trees
5. Tree figures (pdf format)
The above are available for the following analyses:
A. Mixed-marker dataset ‘2Nc3Mt’, one tree
B. Mixed-marker dataset ‘2Nc3Mt’, one tree; Micropygia schomburgkii excluded
C. Mixed-marker dataset ‘2Nc3Mt’, separate mitochondrial (‘3Mt’) and nuclear marker trees (RAG1 and bFib7)
D. Protein coding dataset ‘MtProt’ from entire mitochondrial genomes
The files are thus the following, sorted according to dataset:
A1 Beast_input_2Nc3Mt_1tree.xml
A2 Beast_output_2Nc3Mt_1tree.log
A3 Beast_output_2Nc3Mt_1tree.raw.trees
A4 Beast_output_2Nc3Mt_1tree.max_clade_cred_burnin10M.trees
A5 Tree_2Nc3Mt_1tree.max_clade_cred_burnin10M.pdf
B1 Beast_input_2Nc3Mt_exclMicropygia_1tree.xml
B2 Beast_output_2Nc3Mt_exclMicropygia_1tree.log
B3 Beast_output_2Nc3Mt_exclMicropygia_1tree.raw.trees
B4 Beast_output_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.trees
B5 Tree_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.pdf
C1 Beast_input_2Nc3Mt_separate_trees.xml
C2 Beast_output_2Nc3Mt_separate_trees.log
C3 Beast_output_2Nc3Mt_RAG1.raw.trees
C3 Beast_output_2Nc3Mt_bFib7.raw.trees
C3 Beast_output_2Nc3Mt_mt.raw.trees
C4 Beast_output_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees
C4 Beast_output_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees
C4 Beast_output_2Nc3Mt_mt.max_clade_cred_burnin10M.trees
C5 Tree_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees.pdf
C5 Tree_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees.pdf
C5 Tree_2Nc3Mt_mt.max_clade_cred_burnin10M.trees.pdf
D1 Beast_input_MtProt_1tree.xml
D2 Beast_output_MtProt_1tree.log
D3 Beast_output_MtProt_1tree.raw.trees
D4 Beast_output_MtProt_1tree.max_clade_cred_burnin1M.trees
D5 Tree_MtProt_1tree.max_clade_cred_burnin1M.pdf
Or, sorted according to file type:
1A Beast_input_2Nc3Mt_1tree.xml
1B Beast_input_2Nc3Mt_exclMicropygia_1tree.xml
1C Beast_input_2Nc3Mt_separate_trees.xml
1D Beast_input_MtProt_1tree.xml
2A Beast_output_2Nc3Mt_1tree.log
2B Beast_output_2Nc3Mt_exclMicropygia_1tree.log
2C Beast_output_2Nc3Mt_separate_trees.log
2D Beast_output_MtProt_1tree.log
3A Beast_output_2Nc3Mt_1tree.raw.trees
3B Beast_output_2Nc3Mt_exclMicropygia_1tree.raw.trees
3C Beast_output_2Nc3Mt_RAG1.raw.trees
3C Beast_output_2Nc3Mt_bFib7.raw.trees
3C Beast_output_2Nc3Mt_mt.raw.trees
3D Beast_output_MtProt_1tree.raw.trees
4A Beast_output_2Nc3Mt_1tree.max_clade_cred_burnin10M.trees
4B Beast_output_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.trees
4C Beast_output_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees
4C Beast_output_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees
4C Beast_output_2Nc3Mt_mt.max_clade_cred_burnin10M.trees
4D Beast_output_MtProt_1tree.max_clade_cred_burnin1M.trees
5A Tree_2Nc3Mt_1tree.max_clade_cred_burnin10M.pdf
5B Tree_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.pdf
5C Tree_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees.pdf
5C Tree_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees.pdf
5C Tree_2Nc3Mt_mt.max_clade_cred_burnin10M.trees.pdf
5D Tree_MtProt_1tree.max_clade_cred_burnin1M.pdf
Note about the tree figures (pdf format): Nodes marked with a black circle are supported by a posterior probability (PP) of 1.0, for lower PP the number is given at the node. Blue bars represent the 95% highest posterior density intervals of the node age. MYA = Million years ago.
/Martin Stervander ([email protected])</p
Diversification history and morphological evolution of larks
No full textLarks (Alaudidae) constitute one of the avian families best adapted to xeric environments, having colonized a wide suite of open habitats including deserts. Although their highest diversity is in Africa, larks occur on all nonpolar continents. We tested whether larks exhibit exceptional and/or correlated shifts in the tempos of speciation and ecological trait diversification in the face of open ecological space. We employed a near-complete phylogeny and a morphological dataset including several recently recognized species. We found homogeneity in diversification dynamics across the family and evidence for a diversity‐dependent slowdown in cladogenesis, which indicates that Alaudidae may approach their ‘ecological limit’. We did not observe an early burst in phenotypic diversification, as would be expected in a ‘classic’ adaptive radiation. Our findings suggest that the morphology of larks shows a high level of evolutionary conservatism and overall lack of ecomorphological convergence: ecological variables (diet and habitat)—which by contrast display a higher lability—explain little of shape/size variation except beak shape. Both adaptation to aridity and dietary transitions have evolved independently in multiple lineages across subfamilies. This study supports the idea that continental radiations in open habitats may reach an equilibrium faster than those in tropical forests, due to differences in ecological opportunities.V.G.N. was supported by the ‘Ramón y Cajal’ programme (ref. RYC2019-026703-I) and the research project COMEVO (ref. PID2021-123304NA-I00) of the Spanish Ministry of Science and Innovation. P.A. was supported by the National Swedish Research Council (grant No. 2019-04486) and the Jornvall Foundation.Peer reviewe
Ornis svecica moulting into its new plumage [Ornis svecica i ny fjäderdräkt]
No full textAt the start of the new decade, Ornis Svecia is now entering its 30th year as an ornithological journal. It is a year of change for the journal, perhaps most evident in the transition that started last year with Ornis Svecicamoving from a printed journal to an online journal (Stervander & Svensson 2019). Being digital is a necessary step in today’s publishing landscape and we are happy that we alongside this change also publish all papers as open access, making research available for everyone that is interested. Another major change is that Professor Sören Svensson is stepping down after 29 years as Editor-in-Chief. His role for Ornis Svecica – and indeed for BirdLife Sweden and Swedish ornithology at large – has been profound. During this time the field of ornithology has both widened and specialized. The toolbox of the modern ornithologist now includes molecular biology techniques, advanced miniaturized telemetry loggers, and large-scale weather radar data. But ornithology is still at heart based on careful observation of the natural world, through surveys, ringing and migration studies. The editorial board wishes to express heartfelt thanks to Sören, for his significant efforts.</p
*BEAST species tree 18 ncDNA Sanger markers (Suppl Fig 2)
No full textTree file for Supplementary Figure 2, 18 nuclear (but no mitochondrial) Sanger sequence markers. The tree is in nexus format. A translation table between taxon names used in the file, and taxon names used in the figure is found in the readme file. For further details, see the manuscript
SNP matrix from RAD sequences (nexus format)
No full textMatrix of effectively non-linked and non-automorphic Single Nucleotide Polymorphisms (SNP's) of Cyanistes samples, based on RAD sequences, in nexus format. Key for the sample codes are given in a separate text file
*BEAST species tree 18nc + 2mt DNA Sanger markers (Fig 2a)
No full textTree file for Figure 2a, 18 nuclear and 2 mitochondrial Sanger sequence markers. The tree is in nexus format. A translation table between taxon names used in the file, and taxon names used in the figure is found in the readme file. For further details, see the manuscript
Brief log of RADseq data processing, including custom scripts
No full textBrief work log for analyses of RADseq data. I have used little snippets of custom scripts (which you are free to use and modify), but this log also makes use of plenty of neat little scripts made by other people. One script, by Shannon Hedtke, was modified to fit the purposes in this workflow, and that modified script is provided separately
Alignments of Sanger sequences per locus (nexus format)
No full textLocus-specific alignments of Sanger sequences in nexus format. For information about loci, refer to Supplementary Table 2; for information about individuals/samples, refer to Supplementary Table 1 in the original publication
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