Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome‐wide SNP data from seven native species

Abstract

Since the early Holocene, fish population genetics in the Laurentian Great Lakes have been shaped by the dual influences of habitat structure and post‐glacial dispersal. Riverscape genetics theory predicts that longitudinal habitat corridors and unidirectional downstream water‐flow drive the downstream accumulation of genetic diversity, whereas post‐glacial dispersal theory predicts that fish genetic diversity should decrease with increasing distance from glacial refugia. This study examines populations of seven native fish species codistributed above and below the 58 m high Niagara Falls – a hypothesized barrier to gene flow in aquatic species. A better understanding of Niagara Falls’ role as a barrier to gene flow and dispersal is needed to identify drivers of Great Lakes genetic diversity and guide strategies to limit exotic species invasions. We used genome‐wide SNPs and coalescent models to test whether populations are: (a) genetically distinct, consistent with the Niagara Falls barrier hypothesis; (b) more genetically diverse upstream, consistent with post‐glacial expansion theory, or downstream, consistent with the riverscape habitat theory; and (c) have migrated either upstream or downstream past Niagara Falls. We found that genetic diversity is consistently greater below Niagara Falls and the falls are an effective barrier to migration, but two species have probably dispersed upstream past the falls after glacial retreat yet before opening of the Welland Canal. Models restricting migration to after opening of the Welland Canal were generally rejected. These results help explain how river habitat features affect aquatic species’ genetic diversity and highlight the need to better understand post‐glacial dispersal pathways.

Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern

“…Moderate coverage (e.g., ~10×) short-read sequencing is becoming the predominant approach in conservation genomics (Cam et al, 2020;Galla et al, ;Lado et al, 2020;Lew et al, 2015;Lujan et al, 2020;Oyler-McCance et al, 2015;Robinson et al, 2016). Moderate coverage data sets are generally cost effective and appropriate for characterizing SNPs using a single reference genome, whereas a minimum of 30x coverage is often recommended for de novo SV discovery and genotyping (Ahn et al, 2009;Kosugi et al, 2019;Sims et al, 2014;Wang et al, 2008).…”

Expanding the conservation genomics toolbox: incorporating structural variants to enhance genomic studies for species of conservation concern

“…Low coverage (e.g.,~10x) short-read sequencing currently dominates the field of conservation genomics (Cam et al, 2020;Lado et al, 2020;Lew et al, 2015;Lujan, Weir, Noonan, Lovejoy, & Mandrak, 2020;Oyler-McCance, Cornman, Jones, & Fike, 2015;Robinson et al, 2016). These low coverage datasets are generally cost effective and appropriate for characterizing SNPs using a single reference genome, whereas a minimum of 30x coverage is necessary de novo SV discovery and genotyping (Ahn et al, 2009;Kosugi et al, 2019;Sims, Sudbery, Ilott, Heger, & Ponting, 2014;Wang et al, 2008).…”

Expanding the conservation genomics toolbox: incorporating structural variants to enhance functional studies for species of conservation concern

“…While long-read data coupled with optical mapping is ideal for SV discovery, low coverage (~10x; e.g., Lew et al, 2015;Oyler-McCance et al, 2015;Robinson et al, 2016) and short-read sequencing currently dominates the field of conservation genomics, as it is cost effective and useful for conservation applications using neutral diversity (Cam et al, 2020;Lado et al, 2020;Lujan et al, 2020). While these resources are appropriate to address conservation applications using neutral diversity, it is best to have a minimum of 30x coverage for investigating functional SNPs and/or SVs (Ahn et al, 2009;Kosugi et al, 2019;Sims et al, 2014;Wang et al, 2008).…”

“…Yet, despite the wealth of literature highlighting the promise of incorporating functional diversity into conservation management strategies, the application of genomics to conservation for most species remains focused on assessments of neutral diversity. Over the past 10 years, efforts have largely focused on the transition from microsatellite markers to single nucleotide polymorphisms (SNPs) to increase resolution and power for estimates of gene flow (e.g., Lujan et al, 2020), population structure (e.g., Lado et al, 2020), and neutral genome-wide diversity (Cam et al, 2020).…”