Single nucleotide polymorphism‐based species phylogeny of greater fritillary butterflies (Lepidoptera: Nymphalidae: Speyeria) demonstrates widespread mitonuclear discordance

Abstract

The systematics of Speyeria butterflies has historically been complicated by intraspecific variability that has challenged efforts to delimit species and reconstruct phylogenies. Our study presents a phylogenetic comparison of genomic single nucleotide polymorphisms (SNPs) and mitochondrial COI gene sequences, with comprehensive taxon sampling that includes 15 species and 46 subspecies. Increased sampling of genetic markers and taxa improved the match between genetic clusters, obtained with both phylogenetic and cluster‐based analyses, and species previously detected using morphology, as well as showing two species delimitations that may need revision. We also recovered extensive mitonuclear discordance between genomic SNPs and the COI gene, confirming that mitochondrial DNA does not reliably identify several species at broad geographic scales. Resolution of the relationships of Speyeria species demonstrates the importance of sampling variation across the whole genome, and provides an essential foundation for understanding the evolution of this charismatic clade of North American butterflies.

Systematics and evolution of the African butterfly genus Mylothris (Lepidoptera, Pieridae)

“…Given the factors discussed above, the markers we have used are probably not sufficiently variable to differentiate the closely related species. It is likely that a genomic approach would shed further light on the species boundaries, as has been found in recent studies on nymphalid butterflies (Dinca et al 2019;Campbell et al 2020). Our results do however suggest that radiation within these groups is likely to be recent.…”

Genomic population structure of sympatric sexual and asexual populations in a parasitic wasp, Meteorus pulchricornis (Hymenoptera: Braconidae), inferred from six hundred single‐nucleotide polymorphism loci

“…We focused on the results from the data set with 94% similarity. In general, lower values of the similarity threshold will be appropriate in the case of highly divergent or highly polymorphic populations, while higher values will be more suitable for closely related or less polymorphic populations (Campbell et al, 2020). Since the number of loci was similar among the different similarity thresholds, we used the highest values.…”

Reconciling genomic and ecological species delimitation using a confusing group of butterflies

“…Specimens were collected using aerial nets and were either preserved in ethanol or frozen at -20°C until DNA was extracted from each sample. Following Campbell et al (2019), morphological identifications to subspecies were made using multiple sources, including range information (Moeck 1975), field markings (Bird et al 1995;Brock & Kaufman 2003;Dunford 2009;Warren et al 2012), and comparison to specimens in the Bean Museum collection at Brigham Young University or the personal reference collection of E. Gage. In addition to specimens of S. atlantis and S. hesperis , we included several specimens of S. zerene to test for both ancient and contemporary admixture, since SNP-based Structure analysis by Campbellet al…”

“…DNA extraction, mitochondrial COI gene amplification, ddRAD (Peterson et al 2012) and two-enzyme GBS (Poland et al2012) library preparation and sequencing, and initial mitochondrial and SNP data processing follows Campbell et al (2017Campbell et al ( , 2019) and so are not described in detail here. SNPs were genotyped de novousing the Stacks v. 2.3 pipeline (Catchen et al 2011;Rochetteet al 2019) with default parameter settings except for the following: the n parameter, which controls the number of mismatches tolerated per locus during catalog construction incstacks , was set to 2 instead of 1; we only retained loci that were found in 80% of any single population (the "r80" principle of Paris et al 2017); and a single, random SNP from each locus was output during final processing in the populations program of Stacks to reduce genomic linkage.…”

“…Additionally, Campbellet al (2019) have recently shown, based on a limited number of specimens, substantial genomic divergence in SNPs between S. hesperis populations occurring north and east of the Rocky Mountains (throughout British Columbia, Alberta, and Saskatchewan in Canada and Montana and South Dakota in the United States; hereafter referred to as the "northern lineage"), and those occurring throughout the southwestern and Great Basin regions of the United States ("southern lineage"). Further phylogenetic complexity is provided by interactions with species that have not historically been considered part of this complex, including intermediates between S. hesperis and S. zerene (Boisduval, 1852) (Campbell et al 2019). This may have important implications for conservation initiatives for S. zerene , which has multiple subspecies experiencing significant population declines in western regions where S. hesperis andS.…”