Single-nucleotide polymorphism data describe contemporary population structure and diversity in allochronic lineages of pink salmon (Oncorhynchus gorbuscha)

Abstract

Pink salmon, the most abundant Pacific salmon, have an obligate 2-year life cycle that leads to reproductively isolated even- and odd-year lineages. Using new and existing data, we examined the genetic structure of both lineages across their distributional range by genotyping 16 681 single-nucleotide polymorphisms for 383 individuals originating from seven pairs of even- and odd-year populations. Distinct differences in standing pools of genetic variation were identified between the lineages; we observed higher levels of heterozygosity, allelic richness, and significantly more private alleles in the odd-year lineage. However, the patterns of population structure were concordant between lineages: the Asian and northern Alaska populations displayed little differentiation but differed significantly from populations in southcentral Alaska and the Pacific Northwest. Our population structure results, in the context of known paleoecological information, suggest that both lineages occupied a northern Beringial refugium as well as a Cascadian refugium in North America during the Last Glacial Maximum. These results highlight the influence of historical patterns of habitat availability on contemporary population structure and support the hypothesis of a pre-glacial origin of the lineages.

Freezing ovarian fluid does not alter how it affects fish sperm swimming performance: creating a cryptic female choice ‘spice rack’ for use in split‐ejaculate experimentation

“…This would enable a variety of OF samples to be obtained for use in split‐ejaculate designs. For example, pink salmon ( Oncorhynchus gorbuscha ) have a strict 2‐year life cycle and there is genetically more difference between even‐ and odd‐year spawners within a watershed, than there is across vast geographical ranges (Tarpey et al ., ). OFs could be frozen from several even‐year spawning rivers, followed in a subsequent year by odd‐year spawners and then in future years compared to see if even‐year spawners have sperm that respond differently to even‐year vs .…”

“…Experiments focusing on the nuances of gamete interactions are limited by the ability to obtain fresh samples. For example, comparisonsTarpey et al, 2017). OFs could be frozen from several even-year spawning rivers, followed in a subsequent year by odd-year spawners and then in future years compared to see if even-year spawners have sperm that respond differently to evenyear vs. odd-year OF.Although practical applications for storing biologically active OF would likely require longer-term storage, we froze our samples at -20 C for a restricted time period (~30 min) only.…”

Intraspecific DNA contamination distorts subtle population structure in a marine fish: Decontamination of herring samples before restriction‐site associated sequencing and its effects on population genetic statistics

“…A modest number of clean reference samples can be used to construct a baseline for comparison with potentially contaminated samples using the simple metric of H I . Furthermore, H I is a standard metric that is commonly reported in population genetic studies (Hoffman et al, 2014;Kjeldsen et al, 2016;Tarpey et al, 2017). To our knowledge, this is the one of the first studies of wild populations to examine patterns of H I as a quality-control measure, even though a related metric (ratio of heterozygous/nonreference homozygous sites) is commonly used in the quality control of human genomic data (Wang, Raskin, Samuels, Shyr, & Guo, 2015).…”

Landscape genetics reveal broad and fine‐scale population structure due to landscape features and climate history in the northern leopard frog (Rana pipiens) in North Dakota

“…Prehistoric climatic trends have played large roles in shaping the current biogeographic population structures of many North American species from a wide variety of lineages, including trees (Roberts & Hamann 2015), aquatic insects (Peterson, O'Grady, & Resh, 2017), fish (David & Wright, 2017;Tarpey et al, 2018), and mammals (Puckett, Etter, Johnson, & Eggert, 2015;Sim et al, 2016). As exothermic vertebrates dependent on both terrestrial and aquatic environments, amphibians are particularly susceptible to changes in the environment (Araújo et al, 2008;Mushet, Euliss, Chen, & Stockwell, 2013;Zeisset & Beebee, 2008).…”