Decoupling contamination and hybridization to characterize population structure in Puget Sound rockfishes (Sebastes spp.)

Abstract

Genetic population structure analysis can provide crucial information about marine species’ connectivity that is key to effective management and recovery efforts. Natural hybridization can bias patterns of population structure, although advances in molecular technologies now allow individual-based and genome-wide analyses that facilitate the detection of such interactions. Nevertheless, even advanced molecular genetic methods are still highly sensitive to errors during the processing and bioinformatic filtering of data, including cross-sample contamination and initial data filtering. Signals of contamination are exceptionally difficult to identify especially in hybridizing species, especially when processed and sequenced simultaneously. Here, we investigated the effect of hybridization on spatial genetic structure in three hybridizing rockfish species – Brown Rockfish (Sebastes auriculatus), Copper Rockfish (S. caurinus), and Quillback Rockfish (S. maliger) – in Puget Sound, Washington. Initial analyses indicated potential cross-sample contamination, so we first had to detect and remove contaminated individuals. In Chapter 1, we crafted a method to evaluate individuals for signatures of contamination using allelic balance, or the ratio of reads supporting reference and alternate alleles in heterozygous genomic positions. This method is independent of typical hybrid signals, removing only the individuals with extreme deviation in allelic balance metrics. We also found that minor allele frequency filtering has substantial impact on a dataset, demonstrating that retention of low-frequency alleles may result in weak population differentiation. In Chapter 2, we used remaining ‘clean’ samples to investigate genetic population structure. Hybridization was generally widespread at low levels in Puget Sound and was asymmetric from Quillback Rockfish into Brown Rockfish and Copper Rockfish. We further confirmed Admiralty Inlet as an important bathymetric barrier that isolates populations and retains hybrids in Puget Sound but, in contrast to earlier studies, found no evidence for increased incidence of hybridization in peripheral basins of Puget Sound. However, we detected a genetically differentiated population of Copper Rockfish in Hood Canal. Altogether, our results demonstrated genetic structure and limited dispersal in all species, some but not all of which was due to hybridization. Our results have meaningful implications for future management and conservation of these species, especially concerning the design of species recovery efforts and any potential designation of spatial management units.