(a) Maximum likelihood tree from whole mitochondrial genomes of Xerces Blue, Silvery Blue, and Green-Underside Blue. Node labels are bootstrap support values. (b) Time-calibrated phylogeny from …
The PCA was generated with nuclear DNA data (N = 6,682,591 SNPs (single nucleotide polymorphisms)) from 11 historical butterfly specimens (4 G. xerces and 7 G. lygdamus), a modern G. lygdamus from …
The two historical samples are those with higher average coverage. Individual PSMC plots were bootstrapped 100 times each (lighter lines). One year of generation time and a mutation rate of µ = 1.9 …
(a) PSMC of Xerces Blue L05 down-sampled to half (red) and 75% of coverage (green). (b) PSMC of down-sampled Xerces Blue L05 corrected. Lower-coverage results in underestimation of heterozygote site …
(a) Percentage of the autosomal genome in RoH by size bins: very short RoH (<100 kb), short RoH (100–500 kb), intermediate RoH (500 kb to 1 Mb), and long (1–5 Mb). Short RoH reflect LD patterns, …
(a) Heterozygosity estimates for low-coverage data from both Silvery Blue (historical and modern), Xerces Blue butterflies, and Green-Underside Blue (modern). (b) RoH for each individual classified …
(a) Wide genome Ka/Ks ratio comparison. (b) High-to-moderate effect variant comparison in homozygous sites. (c) High-to-moderate effect variant comparison in heterozygous sites. (d) Presence of …
Genome # | Species | Subspp. | State | Locality | Date | Collection |
---|---|---|---|---|---|---|
USNMENT101413 | G. xerces | California | San Francisco | NA | Barnes | |
USNMENT101402 | G. xerces | California | San Francisco | 16/4/1923 | Barnes | |
USNMENT101441 | G. xerces | California | San Francisco | NA | Barnes | |
USNMENT101406 | G. xerces | California | San Francisco | NA | Barnes | |
USNMENT101434 | G. xerces | California | San Francisco | 16/4/1923 | Barnes | |
USNMENT00181297 | G. lygdamus | incognitus | California | Marin Country | NA | Barnes |
USNMENT00181298 | G. lygdamus | incognitus | California | Fairfax | 27/5/1932 | WMD Field |
USNMENT00181299 | G. lygdamus | incognitus | California | Oakland | 14/4/1948 | Graham Heid |
USNMENT00181300 | G. lygdamus | incognitus | California | San Jose | 27/3/1964 | Opler |
USNMENT00181301 | G. lygdamus | incognitus | California | Haywood City | 1/5/1931 | WMD Field |
USNMENT00181302 | G. lygdamus | incognitus | California | Santa Cruz | 1/4/1932 | JW Tilden/Field |
USNMENT00181303 | G. lygdamus | incognitus | California | Santa Cruz | 8/4/1927 | GW Rawson |
Mapping statistics of the four historical G. xerces (L003, L005, L007, and L009) and the seven historical G. lydagmus (L002, L004, L006, L008, L011, L012, and L013) specimens mapped against the G. …
Sample identifier | Generated reads | Q25 unique mapped reads | Breadth of coverage (%) | Average depth covered regions |
---|---|---|---|---|
L002 | 300,294,248 | 23,337,751 | 37.27 | 5.105 |
L003 | 405,198,060 | 32,547,820 | 36.86 | 6.78 |
L004 | 357,165,438 | 28,722,185 | 38.77 | 6.55 |
L005 | 776,312,378 | 56,459,037 | 45.7 | 12.42 |
L006 | 359,520,168 | 28,498,720 | 40.07 | 6.18 |
L007 | 348,916,870 | 26,758,356 | 34.79 | 6.21 |
L008 | 508,120,156 | 32,107,192 | 42.08 | 7.422 |
L009 | 322,955,384 | 39,312,617 | 40.6 | 8.02 |
L011 | 236,886,534 | 24,165,282 | 38.6 | 5.40 |
L012 | 328,359,669 | 18,683,738 | 33.37 | 4.29 |
L013 | 385,635,644 | 52,612,937 | 47.2 | 12.3 |
Genomic coordinates in G. alexis reference genomes of different wing colouration genes described in other butterfly species.
Chromosome | Start | End | Gene |
---|---|---|---|
FR990043.1 | 5,387,706 | 5,403,599 | Wnt1 |
FR990043.1 | 5,417,902 | 5,423,677 | Wnt6 |
FR990043.1 | 5,519,353 | 5,539,737 | Wnt10b |
FR990043.1 | 5,553,666 | 5,554,753 | Wnt10a |
FR990043.1 | 26,972,856 | 26,974,487 | WntA |
FR990046.1 | 2,343,467 | 2,357,667 | Wnt7b |
FR990046.1 | 6,255,275 | 6,271,623 | Wnt5b |
FR990046.1 | 19,475,636 | 19,486,554 | Wnt9 |
FR990050.1 | 16,200,978 | 16,212,495 | Wnt11 |
FR990054.1 | 20,633,400 | 20,655,261 | Cortex |
FR990059.1 | 20,254,460 | 20,255,275 | Optix |
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 |
Specimen | Wolbachia genus reads | Wolbachia spp. reads |
---|---|---|
L002 | 190 | 5 |
L003 | 131 | 3 |
L004 | 213 | 5 |
L005 | 311 | 8 |
L006 | 242 | 9 |
L007 | 152 | 2 |
L008 | 414 | 21 |
L009 | 236 | 6 |
L011 | 184 | 9 |
L012 | 168 | 9 |
L013 | 523 | 24 |
Additional information on the genomics analyses.
(a) DNA metric. (b) Mappability of the reference genomes. (c) Mitochondrial DNA genomes used in the phylogenetic analysis. (d) Heterozygosity, homozygosity, and runs of homozygosity (RoH). (e) Genes in uncovered genomic regions in Xerces Blue.