RÉSUMÉ
Sea lamprey (Petromyzon marinus) is an invasive species that is a significant source of mortality for populations of valued fish species across the North American Great Lakes. Large annual control programs are needed to reduce the species' impacts; however, the number of successfully spawning adults cannot currently be accurately assessed. In this study, effective breeding size (N b) and the minimum number of spawning adults (N s) were estimated for larval cohorts from 17 tributaries across all five Great Lakes using single nucleotide polymorphisms (SNP) genotyped via RAD-capture sequencing. Reconstructed larval pedigrees showed substantial variability in the size and number of full- and half-sibling groups, N b (<1-367), and N s (5-545) among streams. Generalized linear models examining the effects of stream environmental characteristics and aspects of sampling regimes on N b and N s estimates identified sample size, the number of sampling sites, and drainage area as important factors predicting N b and N s. Correlations between N b, N s, and capture-mark-recapture estimates of adult census size (N c) increased when streams with small sample sizes (n < 50) were removed. Results collectively indicate that parameters estimated from genetic data can provide valuable information on spawning adults in a river system, especially if sampling regimes are standardized and physical stream covariates are included.
RÉSUMÉ
The sea lamprey (Petromyzon marinus) is an invasive species in the Great Lakes and the focus of a large control and assessment program. Current assessment methods provide information on the census size of spawning adult sea lamprey in a small number of streams, but information characterizing reproductive success of spawning adults is rarely available. We used RAD-capture sequencing to genotype single nucleotide polymorphism (SNP) loci for ~1600 sea lamprey larvae collected from three streams in northern Michigan (Black Mallard, Pigeon, and Ocqueoc Rivers). Larval genotypes were used to reconstruct family pedigrees, which were combined with Gaussian mixture analyses to identify larval age classes for estimation of spawning population size. Two complementary estimates of effective breeding size (N b), as well as the extrapolated minimum number of spawners (N s), were also generated for each cohort. Reconstructed pedigrees highlighted inaccuracies of cohort assignments from traditionally used mixture analyses. However, combining genotype-based pedigree information with length-at-age assignment of cohort membership greatly improved cohort identification accuracy. Population estimates across all three streams sampled in this study indicate a small number of successfully spawning adults when barriers were in operation, implying that barriers limited adult spawning numbers but were not completely effective at blocking access to spawning habitats. Thus, the large numbers of larvae present in sampled systems were a poor indicator of spawning adult abundance. Overall, pedigree-based N b and N s estimates provide a promising and rapid assessment tool for sea lamprey and other species.
RÉSUMÉ
Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal homologies between lake trout and other salmonids of varying divergence. The resulting linkage map contains 15,740 single nucleotide polymorphisms (SNPs) mapped to 42 linkage groups, likely representing the 42 lake trout chromosomes. Female and male linkage group lengths ranged from 43.07 to 134.64 centimorgans, and 1.97 to 92.87 centimorgans, respectively. We improved the map by determining coordinates for 41 of 42 centromeres, resulting in a map with 8 metacentric chromosomes and 34 acrocentric or telocentric chromosomes. We use the map to localize the sex determination locus and multiple quantitative trait loci (QTL) associated with intraspecific phenotypic divergence including traits related to growth and body condition, patterns of skin pigmentation, and two composite geomorphometric variables quantifying body shape. Two QTL for the presence of vermiculations and spots mapped with high certainty to an arm of linkage group Sna3, growth related traits mapped to two QTL on linkage groups Sna1 and Sna12, and putative body shape QTL were detected on six separate linkage groups. The sex determination locus was mapped to Sna4 with high confidence. Synteny analysis revealed that lake trout and congener Arctic char (Salvelinus alpinus) are likely differentiated by three or four chromosomal fissions, possibly one chromosomal fusion, and 6 or more large inversions. Combining centromere mapping information with putative inversion coordinates revealed that the majority of detected inversions differentiating lake trout from other salmonids are pericentric and located on acrocentric and telocentric linkage groups. Our results suggest that speciation and adaptive divergence within the genus Salvelinus may have been associated with multiple pericentric inversions occurring primarily on acrocentric and telocentric chromosomes. The linkage map presented here will be a critical resource for advancing conservation oriented genomic research on lake trout and exploring chromosomal evolution within and between salmonid species.