Comparative genomic analyses and a novel linkage map for cisco (Coregonus artedi) provide insights into chromosomal evolution and rediploidization across salmonids

Abstract

26Whole-genome duplication (WGD) is hypothesized to be an important evolutionary 27 mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both 28 diploidy and residual tetraploidy simultaneously are of particular interest, as understanding the 29 mechanisms that maintain this mosaic of ploidy after WGDs may provide important insights into 30 evolutionary processes. Salmonids are a useful model to study the effect of WGDs due to the 31 extensive diversity that has evolved following an ancestral autotetraploidization event. Although 32 most of the salmonid genome has reverted to diploidy following WGD, approximately 25% of 33 the chromosomes continue to exist in a state of residual tetrasomy. In this study, we generate a 34 novel linkage map for cisco (Coregonus artedi) and conduct comparative genomic analyses to 35 refine our understanding of chromosomal fusion/fission history across salmonids. Additionally, 36we propose a new naming strategy, protokaryotypes, that facilitates comparisons across 37Salmonids by standardizing naming to ancestral chromosomes from northern pike (Esox lucius). 38The female linkage map for cisco contains 20,450 loci, 3,383 of which are likely contained 39 within residually tetraploid regions of the genome. Comparative genomic analysis revealed that 40 patterns of residual tetrasomy are generally conserved across species, but there is interspecific 41 variation in the relative extent of the residual tetrasomy. Additionally, with the current reference 42 genomes available, we only find evidence of residual tetrasomy in seven of the eight 43 chromosomes that have been previously hypothesized to show this pattern. This interspecific 44 variation may have important implications for understanding salmonid evolutionary histories and 45 informing future conservation efforts. 46 47

Genotyping‐by‐sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes

“…We used a p-crit of 0.05 for the RAD dataset (Waples, Larson, & Waples, 2016) and 0.02 for the microsatellite dataset (Waples & Do, 2010). For the RAD dataset, only comparisons between sampled loci that were found on different linkage groups (LGs) of the cisco linkage map (Blumstein et al, 2019) were included to correct for physical linkage (Waples et al, 2016). N e calculations using the linkage disequilibrium method can be biased slightly down- 1,000 generations (m = 0.001, m = 0.0005, and m = 0.0001, respectively) and followed by 5, 10, or 15 generations of one of three higher migration (i.e., hybridization) rates (m = 0.01, 0.05, and 0.10) for every initial level of differentiation.…”

“…guidelines suggested from empirical testing to avoid under-or over-merging loci from RAD datasets(Paris, Stevens, Catchen, & Johnston, 2017; parameter flags: --disable-gapped -m 3 -M 5 -H --max_locus_stacks 4 --model_type bounded --bound_high 0.05).A catalog of consensus loci built from 51 artedi sampled in Lake Huron used for the development of a cisco linkage map(Blumstein et al, 2019) was appended in cstacks with an additional 75 individuals in the C. artedi species complex from across the Great Lakes, including 19 fish used in the current study: five hoyi and four kiyi from the Apostle Islands and five each of nigripinnis-like and zenithicus from various locations across Lake Superior (parameter flags: -n 3 -p 6 -disable_gapped). Locus stacks for each individual were matched to the catalog using sstacks (parameter flag: --disable_gapped), data were oriented by locus in tsv2bam, and reads were aligned to loci and SNPs were called with gstacks.SNPs genotyped in greater than 30% of individuals (parameter flag: -r 0.3) were exported with the subprogram populations in genepop and variant call format (vcf) files.…”

Genotyping-by-sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes

“…We examined genetic differentiation across the genome by pairing our data with the artedi linkage map 309 constructed by Blumstein (2019). Catalog IDs were identical between the current study and Blumstein 310 (2019) therefore no alignment step was needed to compare loci.…”

“…An 347 additional 30 artedi from Stockton Island were genotyped at the 9 microsatellite loci. Paired-end 348 assemblies for each locus are available from Blumstein (2019). 349…”

“…Specifically, we (1) examined genetic differentiation and diversity among putative forms of cisco (2) 160 compared the performance of SNPs and microsatellites in this system, and (3) leveraged a newly built 161 cisco linkage map (Blumstein, 2019) to investigate adaptive divergence among forms. In order to remove 162 the potentially confounding factor of distinguishing spatial genetic structure from form-based genetic 163 structure, we focused on a single region in Lake Superior where multiple forms of cisco are found in 164 sympatry, the Apostle Islands.…”