Fig 1.
Generalized range map of current distributions of the Papilio machaon species complex in North America.
Putative hybrid taxa are indicated with an asterisk. Dashed lines indicate approximate ranges of P. machaon subspecies pertinent to the current study. Map image: public domain from www.simplemappr.net, Papilio joanae holotype photograph: J. Tewell.
Table 1.
Species and specimens examined in this study.
Sample sizes for COI/COII sequence data (SEQ), microsatellites (MSAT), and morphological characters (MORPH). Number in parentheses in sequence data column corresponds to EF-1α.
Table 2.
Summary results from maximum parsimony and maximum likelihood analyses.
Extended and complete data sets are included.
Fig 2.
Fifty percent majority rule consensus trees constructed using Bayesian Inference.
a) Extended EF-1α sequence data for 25 genotypes, and b) extended COI/COII sequence data for 54 haplotypes. Numbers above branches represent bootstrap support (if >50%) for maximum parsimony (first number), maximum likelihood (second number) and Bayesian posterior probability values (third number), for nodes that are consistently resolved among search criteria. Colors in circles correspond to the species possessing each haplotype. EF-1α genotype names reflect the corresponding COI/COII haplotype displayed by each specimen, with an added underscore and number indicating cases where specimens that shared COI/COII haplotypes had more than one different EF-1α genotype. Age estimates using COI/COII data for major nodes (numbered black circles) are provided in Table 4.
Fig 3.
STRUCTURE results for microsatellite genotype data.
a) k = 2 based on overall dataset; b) and c) k = 2 and k = 4, respectively, for the polyxenes/zelicaon-like cluster from the overall k = 2; and d) k = 5 for the machaon-like cluster from the overall k = 2 (individuals with ≥70% P. machaon ancestry). Inset indicates the major mtDNA clade (P. machaon, P. polyxenes, P. zelicaon, or the main hybrid clade within the P. machaon clade) for each individual (gaps indicate specimens genotyped for microsatellites that were not sequenced for COI/COII). Alternating black and grey bars above and below the P. machaon portion of d) indicate subspecies; from left to right: P. m. pikei, aliaska, hudsonianus, bairdii, dodi, oregonius, gorganus, and hippocrates.
Table 3.
FST and heterozygosity values based on microsatellite data.
FST comparisons based on microsatellite data between species in bottom triangle, heterozygosity values within each species on diagonal (observed/expected).
Fig 4.
DAPC of putative hybrids and parental taxa generated from microsatellite data.
Inset illustrates the relative contribution of individual discriminant functions (DFs) to overall variability, and the density plots of the two plotted DFs are shown outside of the main plot.
Fig 5.
Multiple correspondence analysis of six morphological characters.
Plotted using the jitter function to improve visualization of overlapping points (non-jittered results shown in Fig. E in S1 File).
Table 4.
Age estimates and 95% confidence intervals of major nodes shown in Fig 2.
All ages in millions of years.
Fig 6.
Approximate maximum glacial extent during the early- to mid-Pleistocene, hypothesized glacial refugia and hybrid origins.
Arrows indicate hypothesized postglacial recolonization routes of hybrids (colored arrows), and parental species (black arrows). Hybrid origins with question marks indicate origins with less geographic certainty. Map image: public domain from www.simplemappr.net.
Fig 7.
Summary of parental similarity and distinctiveness of four putative hybrid lineages with morphological, genetic, and ecological data.
Colored boxes denote similarity or clustering with parental species, or distinctness of the hybrid lineage. Morphology is based on clustering in morphological analysis (MCA). mtDNA is based on mitochondrial DNA clades (note that the unique hybrid clade is identified as both distinct and as P. machaon-like). MSATs STR is based on summarized ancestry at the finest subpopulation scale in STRUCTURE analyses, and MSATs DAPC on summarized clustering in DAPC analyses. Range shows sympatry or parapatry with parental species, flight period shows overlapping adult flight period, habitat is based on a general assessment of shared habitat type (forest openings, strict hilltopping behavior, under forest cover, etc.), and host plant shows shared larval host. Boxes with wide outlines indicate uncertainty in particular characteristics. Ecological information is presented in more detail in Table D in S1 File.