We examined the genetic structure and phylogeography of populations of the stonefly Peltoperla tarteri in the Southern Appalachians to determine the extent and likely mechanism for dispersal of this stream insect. A 454-base-pair (bp) portion of the mitochondrial control region was sequenced from a minimum of 20 individuals from eight populations. Pairwise FST and exact tests showed high levels of differentiation among almost all populations except those on the same stream. amova analysis detected significant genetic differentiation between streams within drainages (phi(SD) = 0.14, P < 0.001), and there was a slight positive correlation between aquatic distance and genetic distance (r = 0.295, P = 0.03). According to nested clade analysis, the present day pattern of genetic variation in P. tarteri is the result of a historical range expansion coupled with restricted gene flow with isolation by distance. Together, these analyses suggest that adult dispersal is limited and that movement by larvae is the primary dispersal mechanism for P. tarteri.

Summary 1. Gene flow and dispersal among populations of a stone‐cased caddis (Tasimiidae: Tasimia palpata) were estimated indirectly using a 460 bp region of the cytochrome oxidase I gene of mitochondrial DNA. 2. There was no significant differentiation at the largest spatial scale (between catchments) and no correlation between genetic distance and geographic distance. These results are consistent with widespread adult dispersal. 3. Conversely, significant genetic differentiation was detected at the smallest spatial scale examined (among reaches within streams). This pattern was primarily because of significant FST values in a single stream (Bundaroo Creek). 4. Bundaroo Creek also had the lowest mean number of haplotypes per population (n = 7) suggesting that a limited number of females may be responsible for recruitment at these sites. Significant FST's at the reach scale may be a result of this ‘patchy’ recruitment. However, additional evidence regarding the long‐range dispersal ability and fecundity of T. palpata females is needed to test this hypothesis fully.

Low levels of primary sequence similarity across insect taxa have led to the suggestion of conserved structural elements in the insect mitochondrial control region. Our aim was to determine whether previously described motifs and secondary structures exist in stoneflies (Plecoptera). Several motifs and structural elements previously described in Orthoptera and Diptera were found, including a conserved 'hairpin' structure that may play a role in the initiation of mtDNA replication. The repeat region had the highest percentage similarity, lowest A-T content and highest transition to transversion ratio, suggesting a unique evolutionary pattern for the repeats. Finally, we discuss the usefulness of the control region in population genetic and evolutionary studies.

1. Genetic techniques are being used increasingly to address questions about dispersal and gene flow of freshwater invertebrates. However, population genetic structure can be affected by factors other than dispersal. Many stream insects have long life cycles that result in the simultaneous existence of multiple cohorts throughout the larval development period. If larval development is fixed, successive cohorts may be reproductively isolated and, as a result, genetically distinct. In such cases, significant levels of genetic differentiation between cohorts could confound estimates of dispersal based on population genetic structure. 2. Peltoperla tarteri is a stonefly that can be abundant in Appalachian headwater streams. Although P. tarteri is univoltine at the type locality (Big Paint Hollow, WV, U.S.A.), the study populations in southwestern Virginia, U.S.A., were semivoltine. This semivoltine life cycle results in the simultaneous existence of multiple cohorts with the potential for significant genetic differentiation among them. 3. Levels of genetic differentiation among P. tarteri cohorts were analysed with mitochondrial DNA (mtDNA) sequence data from the non‐coding origin of replication or `control' region from 93 individuals from two successive cohorts (collected in 1998 and 1999). 4. Analysis of molecular variance (AMOVA) indicated no genetic differentiation among cohorts (FST=0.0), and gene flow among cohorts was very high (Nm=∞). 5. High levels of gene flow among cohorts suggest that larval development of P. tarteri is not fixed. Gene flow among cohorts most likely occurs as a result of a cohort split in which some individuals complete development in one or three years instead of two.