Phylogeographical break and limited connectivity between multiple refugia in panantarctic moss species

This file was generated on 2022-05-06 by MARTA SAŁUGA

GENERAL INFORMATION

 1. Title of Dataset: Phylogeographical break and limited connectivity between multiple refugia in panantarctic moss species

 2. Author Information

      A. Principal Investigator Contact Information

            Name: Marta Saługa

            Institution: W. Szafer Institute of Botany, Polish Academy of Sciences

            Address: Lubicz 46, 31-512 Kraków Poland

            Email: m.saluga@botany.pl

      B. Associate or Co-investigator Contact Information

            Name: Ryszard Ochyra

            Institution: W. Szafer Institute of Botany, Polish Academy of Sciences

            Address: Lubicz 46, 31-512 Kraków Poland

            Email: r.ochyra@botany.pl

            Name: Michał Ronikier

            Institution: W. Szafer Institute of Botany, Polish Academy of Sciences

            Address: Lubicz 46, 31-512 Kraków Poland

            Email: m.ronikier@botany.pl

3. Date of data collection (single date, range, approximate date): several Antarctic expeditions between 1940 and 2016 

4. Geographic location of data collection: Antarctica, South America: Chilean and Argentine Patagonia, Australia (Victoria), New Zealand (South Island) 

5. Information about funding sources that supported the collection of the data: specimens are deposited in the bryological herbarium of the Institute of Botany, Polish Academy of Sciences; funds of the W. Szafer Institute of Botany of the Polish Academy of Sciences  

DATA & FILE OVERVIEW

1. File List:

1) ALIGNMENT_ITS Phylogeography 127 SEQ - the matrix used for the phylogenetic analysis and presented in the research article

2) ALIGNMENT_cpDNA Phylogeography 115 SEQ - the matrix used for the phylogenetic analysis and presented in the research article

3) ALIGNMENT_rps4 S. sarconeurum and S. lithophila 123 SEQ - the rps4 sequences retrieved for Syntrichia sarconeurum and Syntrichia lithophila

4) ALIGNMENT_tRNAGly S. sarconeurum and S. lithophila 111 SEQ - the tRNAGly sequences retrieved for Syntrichia sarconeurum and Syntrichia lithophila

5) ALIGNMENT_trnLF S. sarconeurum and S. lithophila 117 SEQ - the trnLF sequences retrieved for Syntrichia sarconeurum and Syntrichia lithophila

6) ALIGNMENT_ITS Haplotype Network 116 SEQ - the matrix used in POPArt v1.7 and presented in the research article

7) ALIGNMENT_cpDNA Haplotype Network 111 SEQ - the matrix used in PopArt v1.7 (Leigh and Bryant, 2015) and presented in the research article

8) ALIGNMENT_ITS Population Genetics 120 SEQ - the matrix used in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010) and presented in the research article

9) ALIGNMENT_rps4 Population Genetics 123 SEQ - the matrix used in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010) and presented in the research article

10) ALIGNMENT_tRNAGly Population Genetics 111 SEQ - the matrix used in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010) and presented in the research article

11) ALIGNMENT_trnLF Population Genetics 117 SEQ - the matrix used in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010) and presented in the research article

12) ALIGNMENT_Concatenated Population Genetics 120 SEQ - the matrix used in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010) and presented in the research article

13) ALIGNEMNT_Patagonia Population Genetics 10 SEQ - the matrix used in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010) and SPAGeDi 1.5 (Hardy and Vekemnas, 2002) and presented in the research article

14) ALIGNMENT_Maritime Antarctic Population Genetics 49 SEQ - the matrix used in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010) and SPAGeDi 1.5 (Hardy and Vekemnas, 2002) and presented in the research article

15) ALIGNMENT_Continental Antarctic Population Genetics 58 SEQ - the matrix used in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010) and SPAGeDi 1.5 (Hardy and Vekemnas, 2002) and presented in the research article

16) ALIGNMENT_Australasia Population Genetics 03 SEQ - the matrix used in Arlequin 3.5.2.2 (Excoffier and Lischer, 2010) and SPAGeDi 1.5 (Hardy and Vekemnas, 2002) and presented in the research article

17) ALIGNMENT_ITS Phylogeny Supplementary Material 65 SEQ - the matrix used for the phylogenetic analysis and presented in the supplementary material being a part of research article

18) ALIGNMENT_cpDNA Phylogeny Supplementary Material 141 SEQ - the matrix used for the phylogenetic analysis and presented in the supplementary material being a part of research article

METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data:

All methods used can be found in Saługa, Ochyra and Ronikier 2022

2. Methods for processing the data:

• MrBayes v3.2 - Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., … Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539–542. https://doi.org/10.1093/sysbio/sys029
• RAxMLGUI v2.0 - Edler, D., Klein, J., Antonelli, A., & Silvestro, D. (2020). raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML. Methods in Ecology and Evolution, 12, 373-377. http://dx.doi.org/10.1111/2041-210X.13512
• BEAST V2.5.0 - Suchard, M. A., Lemey, P., Baele, G., Ayres, D. L., Drummond, A. J., & Rambaut, A. (2018). Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus evolution, 4(1), vey016. http://doi:10.1093/ve/vey016
• jModelTest v2.1.10 - Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nature Methods, 9, 772. https://doi.org/10.1038/nmeth.2109
• SequenceMatrix v1.7.8 - Vaidya, G., Lohman, D. J., & Meier, R. (2011). SequenceMatrix: concatenation software for the fast assembly of multigene datasets with character set and codon information. Cladistics, 27(2), 171-180. https://doi.org/10.1111/j.1096-0031.2010.00329.x
• PopArt v1.7 - Leigh, J. W., & Bryant, D. (2015). Popart: Full-feature software for haplotype network construction. Methods in Ecology and Evolution, 6, 1110–1116. https://doi.org/10.1111/2041-210X.12410 
• Arlequin v3.5.2.2 - Excoffier, L., & Lischer, H. E. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
• SPAGeDi v1.5 - Hardy, O. J., & Vekemans, X. (2002). SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular ecology notes, 2(4), 618-620. https://doi.org/10.1046/j.1471-8286.2002.00305.x
• SeqState v1.4.1 - Simmons, M. P., & Ochoterena, H. (2000). Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology, 49(2), 369-381. https://www.jstor.org/stable/2585224

Funding provided by: Narodowe Centrum Nauki
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100004281
Award Number: Opus 2015/17/B/NZ8/02475