Secondary contact may have important implications for ecological and evolutionary processes; however, few studies have tracked the outcomes of secondary contact from its onset in natural ecosystems. We evaluated an anadromous alewife (Alosa pseudoharengus) reintroduction project in Rogers Lake (Connecticut, USA), which contains a landlocked alewife population that was isolated as a result of colonial era damming. After access to the ocean was restored, adult anadromous alewife were stocked into the lake. We assessed anadromous juvenile production, the magnitude and direction of introgression and the potential for competition between ecotypes. We obtained fin clips from all adult alewife stocked into the lake during the restoration and a sample of juveniles produced in the lake two years after the stocking began. We assessed the ancestry of juveniles using categorical assignment and pedigree reconstruction with newly developed microhaplotype genetic markers. Anadromous alewives successfully spawned in the lake and hybridized with the landlocked population. Parentage assignments revealed that male and female anadromous fish contributed equally to juvenile F1 hybrids. The presence of landlocked backcrosses shows that some hybrids were produced within the first two years of secondary contact, matured in the lake, and reproduced. Therefore, introgression appears directional, from anadromous into landlocked, in the lake environment. Differences in estimated abundance of juveniles of different ecotypes in different habitats was also detected, which may reduce competition between ecotypes as the restoration continues. Our results illustrate the utility of restoration projects to study the outcomes of secondary contact in real ecosystems.

Provided here is the merged VCF file characterizing the variants found in alewife (Alosa pseudoharengus) from anadromous and landlocked populations. There is also a FASTA  file of the reference sequences that were used for mapping derived from mined ddRAD data. This information is required if anyone who amplifies and sequences additional alewife with our developed microhaplotypes (Primers available in Supplementary Table 1). The VCF file is necessary for calling the same variant positions within microhaplotypes that will be passed into the r-package microhaplot, as described in the materials and methods.

In addition we provide the called haplotypes for the anadromous alewife stocked into Rogers lake, the landlocked population before stocking and the juveniles after secondary contact. These calls can directly be used for further downstream analyses as described in the manuscript.

If you require further information please contact Kerry Reid kerryreid13@gmail.com or kreid@ucsc.edu