APPENDICES
APPENDIX 1.
Number of mapped reads and comparative statistics of the BWA multireference iterative mapping using stringent (STR) and relaxed (REL) parameters. (Appendices PDF files available for download.)
APPENDIX 2.
GenBank accession numbers of the Arvicolinae (and outgroups) complete and partial mitochondrial genomes used in the phylogenetic analyses (Figure 3, Appendix 9, Appendix 10). Numbers in italics denote partial genomes, whereas numbers in red indicate sequences used in the BEAST analysis (just one sequence per species has been used). (Appendices PDF files available for download.)
APPENDIX 3.
Best partition schemes and substitution models for RAxML, MrBayes and BEAST analyses inferred using ModelFinder for both datasets [i.e., using consensus Pliomys lenki sequences generated using stringent (STR) and relaxed (REL) BWA mapping parameters]. (Appendices PDF files available for download.)
APPENDIX 4.
GenBank accession numbers of Dinaromys bogdanovi (and outgroups) CYTB sequences used to analyze the possible placement of Pliomys lenki within the diversity of D. bogdanovi (see Appendix 11). (Appendices PDF files available for download.)
APPENDIX 5.
First five hits of the BLASTn analyses of the contig fragments >50 bp recovered in the Pliomys sequence generated using BWA relaxed parameters (REL) that were not recovered using the stringent parameters (STR). Position of the fragments within the mitogenome, length of the sequences, sequences, and hits statistics are indicated. (Appendices PDF files available for download.)
APPENDIX 6.
MapDamage report of the BWA iterative mapping using the usual DNA stringent (STR) and relaxed (REL) mapping parameters to generate the consensus sequences for Pliomys lenki sample ZARADNA 219. The top four panels show the frequency of purines and pyrimidines just before and after the reads, respectively. The middle two panels show accumulation of 5’ C-to-T (red) and 3’ G-to-A (blue) misincorporations. Bottom panel displays the read size distribution of mapped reads. (Appendices PDF files available for download.)
APPENDIX 7.
Partial mitochondrial genome sequence (in fasta format) of Pliomys lenki ZARADNA 219 obtained using stringent BWA mapping parameters (STR sequence). (Appendices txt file available for download.)
APPENDIX 8.
Genome characteristics, missing data and PCGs stop codons of the two mitochondrial genomes generated for Pliomys lenki using stringent (STR) and relaxed (REL) parameters in the BWA iterative mapping. (Appendices PDF files available for download.)
APPENDIX 9.
Maximum Likelihood (ML) trees of Arvicolinae mitochondrial genomes (excluding Control Region) and using the Pliomys lenki consensus sequences generated with regular ancient DNA mapping stringent parameters (STR sequence, left) and with relaxed parameters (REL sequence, right). Numbers in nodes indicate Maximum Likelihood Bootstrap (MLB) values. Circles indicate MLB=100. GenBank accession numbers are listed in Appendix 2 and partitioning scheme in Appendix 3. (Appendices PDF files available for download.)
APPENDIX 10.
Bayesian trees of Arvicolinae mitochondrial genomes (excluding Control Region) and using the Pliomys lenki consensus sequences generated with regular ancient DNA mapping stringent parameters (STR sequence, left) and with relaxed parameters (REL sequence, right). Numbers in nodes indicate Posterior Probability (PP) values. Circles in nodes indicate PP=1. GenBank accession numbers are listed in Appendix 2 and partitioning scheme in Appendix 3. (Appendices PDF files available for download.)
APPENDIX 11.
Maximum Likelihood (ML) trees of a dataset comprising a CYTB fragment (555 bp) for Dinaromys bogdanovi individuals and the two Pliomys lenki sequences generated using stringent (STR) and relaxed (REL) BWA mapping parameters to evaluate the possible inclusion of Pliomys in the D. bogdanovi variability. Numbers in nodes indicate Maximum Likelihood Bootstrap (MLB) values. Just MLB values in selected nodes are displayed. GenBank accession numbers are listed in Appendix 4. D. bogdanovi haplogroups follow Kryštufek et al. (2007). (Appendices PDF files available for download.)
APPENDIX 12.
Comparison of Bayesian Factor (BF) values using estimated marginal likelihood (MLE) values and Path Sampling (PS)/Stepping Stone sampling (SS) approaches for the calibrated dataset. Yule and Birth-Death process competing models were analyzed, being the Yule process strongly supported (following value ranges of Kass and Raftery, 1995). (Appendices PDF files available for download.)
APPENDIX 13.
Comparison of node age estimates and their 95% highest posterior densities (HPDs) between the different estimates obtained by Abramson et al. (2021), Whithnell and Scarpetta (2024) and in this paper (for both Pliomys sequences generated).(Appendices PDF files available for download.)
