Aim: Historical biogeography of the Antarctic terrestrial biota remains poorly studied and understood. We aim to advance this through a range-wide, multilocus analysis of a pan-Antarctic moss species, in the context of its age, range dynamics, phylogeographical structure, and location of possible long-term refugia.

Location: Continental and maritime Antarctic, South America (Patagonia), Australasia.

Taxon: Syntrichia sarconeurum Ochyra & R.H. Zander (Pottiaceae).

Methods: We used a comprehensive, range-wide and taxonomically-informed sampling, and multilocus sequencing of nuclear and plastid DNA regions. Temporal evolutionary framework, regional genetic diversification and diversity were assessed with phylogenetic and phylogeographic reconstructions, molecular dating, haplotype networks, mismatch analysis, and S-DIVA reconstruction of past events and ancestral areas.

Results: Intercontinental disjunction between Australia and Antarctica/S. America was dated to 3.77 Ma, while diversification of extant Syntrichia sarconeurum lineages had taken place since roughly 1.36 Ma. Antarctic populations contained two high-frequency, allopatric cpDNA haplotypes, which highlighted separation of the continental populations. ITS data showed higher diversification and revealed three main lineages with a main genetic break mostly concordant with plastid data. ITS also showed contrasting diversity between the Antarctic continent and maritime Antarctic/Patagonia.

Main conclusions: Age of the Antarctic range of Syntrichia sarconeurum potentially reaches back to mid-Pliocene, while diversification of extant genetic lineages was linked with recurrent macroenvironmental changes of the Pleistocene. Significant phylogeographical structure displays a major genetic break, which coincides with a known boundary in the terrestrial biota and suggests constrained population connectivity. S. sarconeurum persisted in situ over several glacial periods in refugia both in the peripheral maritime Antarctic and within the Antarctic continent. Disparity in genetic diversity among these areas hypothetically reflects asymmetric changes of reproduction mode in the past. Finally, nested topology of Patagonian subclades and ancestry analysis indicates that South American populations were secondary and originated through multiple dispersal from the Antarctic region.

Plant sampling was based on collections gathered during Antarctic expeditions between 1940 and 2016, with specimens deposited in the bryological herbarium of the Institute of Botany, Polish Academy of Sciences (KRAM).

One nuclear ribosomal marker, ITS1-5.8S-ITS2, and three plastid (cpDNA) markers, rps4, tRNAGly, and trnL-F, were selected for the multilocus analysis. Forward and reverse sequences were automatically assembled using Geneious 10.1.3. Sequences of the four DNA regions were individually aligned using the algorithm mafft-auto with the remaining default settings in Mafft (https://mafft.cbrc.jp/alignment/server//). Selected DNA regions were concatenated using SequenceMatrix. For all molecular analyses, indels in DNA sequences were coded and calculated in SeqState v1.4.1 using a simple indel coding. All programs are listed in the ReadMe text file. 

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