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. 2024 Oct 4;12:RP87928. doi: 10.7554/eLife.87928

Key resources table.

Reagent type (species) or resource Designation Source or reference Identifiers Additional information
Biological sample (Glaucopsyche xerces; female) L003 This paper SAMEA114094142 See Materials and methods
Biological sample (G. xerces; male) L005 This paper SAMEA114094143 See Materials and methods
Biological sample (G. xerces; male) L007 This paper SAMEA114094144 See Materials and methods
Biological sample (G. xerces; female) L009 This paper SAMEA114094145 See Materials and methods
Biological sample (Glaucopsyche lygdamus; male) L002 This paper SAMEA114094134 See Materials and methods
Biological sample (G. lygdamus; male) L004 This paper SAMEA114094135 See Materials and methods
Biological sample (G. lygdamus; male) L006 This paper SAMEA114094136 See Materials and methods
Biological sample (G. lygdamus; male) L008 This paper SAMEA114094137 See Materials and methods
Biological sample (G. lygdamus; male) L011 This paper SAMEA114094138 See Materials and methods
Biological sample (G. lygdamus; female) L012 This paper SAMEA114094139 See Materials and methods
Biological sample (G. lygdamus; male) L013 This paper SAMEA114094140 See Materials and methods
Biological sample (G. lygdamus; male) RVcoll10-B005 This paper SAMEA114094141 See Materials and methods
Biological sample (Glaucopsyche alexis; male) G. alexis Hinojosa Galisteo et al., 2021 ilGlaAlex1.1; GCA_905404095.1
Biological sample (Aricia agestis) A. agestis Hayward et al., 2023 LR990279.1
Biological sample (Aricia artaxerxes) A. artaxerxes Ebdon et al., 2022 OW569311.1
Biological sample (Celastrina argiolus) C. argiolus Hayward et al., 2021 LR994603.1
Biological sample (Cyaniris semiargus; male) C. semiargus Lohse et al., 2023 LR994570.1
Biological sample (G. alexis; male) G. alexis Hinojosa Galisteo et al., 2021 FR990065.1
Biological sample (G. xerces) G. xerces Grewe et al., 2021 MW677564.1
Biological sample (Lysandra bellargus; female) L. bellargus Lohse et al., 2022 HG995365.1
Biological sample (Lysandra coridon; male) L. coridon Vila et al., 2023 HG992145.1
Biological sample (Plebejus argus) P. argus Zhou et al., 2020 MN974526.1
Biological sample (Plebejus melissa) P. melissa Ellis et al., 2021 DWQ001000057.1
Biological sample (Plebejus anna) P. anna Ellis et al., 2021 DWTA01000073.1
Biological sample (Polyommatus icarus; male) P. icarus https://www.darwintreeoflife.org/ OW569343.1
Biological sample (Shijimiaeoides divina) S. divina Jeong et al., 2017 NC_029763.1
Biological sample (Zizina emelina) Z. emelina Liu et al., 2020 MN013031.1
Software, algorithm BUSCO Manni et al., 2021 v.5.1.2
Software, algorithm AdapterRemoval Schubert et al., 2016 v.2.2.2
Software, algorithm BWA – backtrack Li and Durbin, 2009 v.0.7.1
Software, algorithm BWA – mem Li, 2013 v.0.7.1
Software, algorithm Qualimap2 Okonechnikov et al., 2016 v.2.2.2
Software, algorithm pmdtools Skoglund et al., 2014 v.0.50
Software, algorithm MapDamage2 Jónsson et al., 2013 v.2.7.12
Software, algorithm Bedtools Quinlan and Hall, 2010 v.2.27.1
Software, algorithm snpAD Prüfer, 2018 v.0.3.2
Software, algorithm GATK McKenna et al., 2010 v.3.5–3.7
Software, algorithm vcftools Danecek et al., 2011 v.0.1.12b–0.1.14b
Software, algorithm angsd Korneliussen et al., 2014 v.0.916
Software, algorithm bcftools Danecek et al., 2021 v.1.9
Software, algorithm Mitofinder Allio et al., 2020 v.1.4
Software, algorithm MACSE Ranwez et al., 2018 v.2.05
Software, algorithm MAFFT Katoh and Standley, 2013 v.7.490
Software, algorithm IQ-TREE2 Minh et al., 2020 v.2.1.3
Software, algorithm ModelFinder Kalyaanamoorthy et al., 2017 Available in IQ-TREE2
Software, algorithm UFBoot2 Hoang et al., 2018 Available in IQ-TREE2
Software, algorithm BEAST2 Bouckaert et al., 2019 v.2.6.3
Software, algorithm bModelTest Bouckaert and Drummond, 2017 v.1.2.1
Software, algorithm Tracer Rambaut et al., 2018 v.1.7.2
Software, algorithm PSMC Li and Durbin, 2011 v.0.6.5
Software, algorithm PCAngsd Meisner and Albrechtsen, 2018 v.20180209
Software, algorithm Bcftools-roh Narasimhan et al., 2016 v.1.9
Software, algorithm SNPeff Cingolani et al., 2012 v.4.3
Software, algorithm Picard Broad Institute, 2015 v.2.0.1
Software, algorithm Samtools Li et al., 2009 v.1.6
Software, algorithm BamUtil Jun et al., 2015 v.1.0.13
Software, algorithm Bedtools Quinlan and Hall, 2010 v.2.27.1
Software, algorithm BLAST Altschul et al., 1990 v.2.2.2
Software, algorithm BBMap Bushnell, 2014 v.38.18
Software, algorithm Prinseq Schmieder and Edwards, 2011 v.0.20.4
Software, algorithm Kraken2 Wood et al., 2019 v.2.1.1
Software, algorithm R R Core Team, 2019 v.3.6.3–4.1.0
Software, algorithm Ggplot2 Wickham, 2016 v.3.0.0