The speciation continuum: Population structure, gene flow, and maternal ancestry in the Simulium arcticum complex (Diptera: Simuliidae)

•We compare black fly populations at different stages of chromosome divergence.•We analyze 11 microsatellite loci and 4 mitochondrial DNA (mtDNA) genes.•Late stage taxa show both nuclear and mtDNA differentiation in allopatry and sympatry.•Intermediate stage taxa show only nuclear differentiation in allopatry and sympatry.•Early stage taxa show panmixia in sympatry and some nuclear divergence in allopatry.

Comparative analyses of populations at different stages of divergence can yield insights into the process of speciation. We assess population structure, gene flow, and maternal ancestry at five locations containing sympatric members of the Simulium arcticum complex at different stages of chromosome divergence. We analyze both nuclear and mitochondrial DNA markers, including 11 microsatellite loci, as well as COI, COII, cytb, and ND4 gene sequences. Simulium negativum, representing the later stages of divergence, shows both nuclear and mitochondrial differentiation when compared with allopatric and sympatric chromosomal forms, as well as both low contemporary and historical gene flow in sympatry. At intermediate stages of chromosome divergence, populations differ at nuclear, but not mitochondrial, loci in allopatry and sympatry. In one comparison of intermediate stage chromosomal forms (S. arcticum sensu stricto and S. apricarium), populations demonstrate low contemporary, but higher historical, gene flow in sympatry. In a second sympatric comparison (S. arcticum s. s. and S. brevicercum), both contemporary and historical gene flow are high. All analyses of sympatric populations at the earliest stages of chromosome divergence demonstrate panmixia; yet, some nuclear differentiation in allopatry is apparent. These findings suggest that molecular divergence is tracking chromosome divergence along a chromosomally-defined continuum of speciation in black flies.

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