An important criterion for understanding speciation is the geographic context of population divergence. Three major modes of allopatric, parapatric, and sympatric speciation define the extent of spatial overlap and gene flow between diverging populations. However, mixed modes of speciation are also possible, whereby populations experience periods of allopatry, parapatry, and/or sympatry at different times as they diverge. Here, we report clinal patterns of variation for 21 nuclear-encoded microsatellites and a wing spot phenotype for cherry-infesting Rhagoletis (Diptera: Tephritidae) across North America consistent with these flies having initially diverged in parapatry followed by a period of allopatric differentiation in the early Holocene. However, mitochondrial DNA (mtDNA) displays a different pattern; cherry flies at the ends of the clines in the eastern USA and Pacific Northwest share identical haplotypes, while centrally located populations in the southwestern USA and Mexico possess a different haplotype. We hypothesize that the mitochondrial difference could be due to lineage sorting but more likely reflects a selective sweep of a favorable mtDNA variant or the spread of an endosymbiont. The estimated divergence time for mtDNA suggests possible past allopatry, secondary contact, and subsequent isolation between USA and Mexican fly populations initiated before the Wisconsin glaciation. Thus, the current genetics of cherry flies may involve different mixed modes of divergence occurring in different portions of the fly’s range. We discuss the need for additional DNA sequencing and quantification of prezygotic and postzygotic reproductive isolation to verify the multiple mixed mode hypothesis for cherry flies, and draw parallels from other systems to assess the generality that speciation may commonly involve complex biogeographies of varying combinations of allopatric, parapatric, and sympatric divergence.

A total of 364 adult flies from populations 1-15 (Fig. 1a; Table S1) were genotyped for 21 microsatellite loci (see Supplemental Methods for details). References for primers and conditions used for PCR amplification can be found in Maxwell et al. (2013) and Michel et al. (2010). Genotyping was performed as described in Saint Jean et al. (2018), with size standards included in each genotyper run, as well as representative eastern R. cingulata and western R. indifferens, to ensure that alleles were properly aligned and comparably scored.

CingIndBiogeo.str
A STRUCTURE file containing called microsatellite genotyopes for all 364 Rhagoletis cingulata and Rhagoletis indifferens individuals.

CingIndBiogeoREADME.csv
A csv file linking the site numbers from the manuscript to the site codes used in the STRUCTURE file.