Historic and modern butterfly genomes
Glaucopsyche alexis was chosen as a congeneric reference to compare the demographic histories of both the Xerces Blue and the Silvery Blue (Fig. 1). We generated a G. alexis reference genome from a male specimen collected in Alcalá de la Selva in Teruel (Spain). Its genome has a sequence length of 619,543,730 bp on 24 chromosomes – including the Z sex chromosome – and the mitochondrial genome (6). The genome sequence is biologically complete (BUSCO v5.1.2 Lepidoptera completeness 97.1%).
We extracted DNA from 12 historical specimens (5 G. xerces , 7G. lygdamus ) (Table S1). One Xerces Blue sample did not yield detectable DNA in two independent extractions. For each of the successful extracts we prepared a single library which was shotgun sequenced on the HiseqX Illumina platform. We mapped 124,101,622 and 184,084,237 unique DNA reads of Xerces Blue and Silvery Blue, respectively, against the G. alexis reference genome (Table S2). The DNA reads exhibited typical ancient DNA features, such as short mean read length (ranging from 47.55 to 67.41 bases on average, depending on the specimen (Fig. S1)) and post-mortem deamination patterns at the 5’ and 3’ ends (Table S2) (Fig. S2). The historical genomes covered 49.3% (Xerces Blue) and 55.2% (Silvery Blue) of the G. alexisreference genome, largely because repetitive chromosomal regions cannot be confidently assessed with short, ancient DNA sequence reads. To estimate the mappable fraction of the reference G. alexis genome, we randomly fragmented it to 50 to 70 nucleotides and mapped the generated fragments back to the complete genome. An average of 57.8% of the G. alexis genome was covered with these read lengths (Fig. S3). We suggest that reduced coverage from the historical specimens may be due to genomic divergence of G. xerces and G. lygdamusfrom the G. alexis reference (Fig. S4).
The sex of the specimens was determined by differential coverage of the Z chromosome (females are the heterogametic sex in the Lepidoptera and show reduced coverage on the Z chromosome). As listed in the original museum records, we found one Silvery Blue and two Xerces Blue females (Table S2). Inter-individual comparisons suggested no close kinship link among the studied individuals.