DOI: 10.5061/dryad.h18931zp3
title: Phylogeographical break and limited connectivity between multiple refugia in panantarctic moss species

description: 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.
description: 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, <em>ITS1-5.8S-ITS2</em>, and
 three plastid (cpDNA) markers, <em>rps4</em>,
 <em>tRNAGly</em>, and
 <em>trnL-F</em>, 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. 
description: 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
 <br> 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
 <br> 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