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Round whitefish (Prosopium cylindraceum) have abroad, disjunct range across northern North America and Eurasia, and little is known about their genetic population structure. We performed genetic analyses of round whitefish from 17 sites across its range using nine microsatellites, two mitochondrial DNA (mtDNA) loci, and 4918 to 8835 single-nucleotide polymorphism (SNP) loci. Our analyses identified deep phylogenetic division between eastern and western portions of the range, likely indicative of origins from at least two separate Pleistocene glacial refugia. Regionally, microsatellites and SNPs identified congruent patterns in subdivision, and population structure was consistent with expectations based on hydrologic connectivity. Within the Laurentian Great Lakes, Lake Huron and Lake Ontario were identified as key areas of interest. Lake Huron appears to be a contemporary source population for several other Great Lakes, and Lake Ontario contains a genetically discrete group of round whitefish. In all cases, multiple genetic markers yielded similar patterns, but SNPs offered substantially enhanced resolution. We conclude that round whitefish have population subdivision on several scales important for understanding their evolutionary history and conservation planning. Les menominis ronds (Prosopium cylindraceum) ont une vaste aire de repartition discontinue dans le nord de l'Amerique du Nord et l'Eurasie, et les connaissances sur la structure genetique de leurs populations sont tres limitees. Nous avons realise des analyses genetiques de menominis ronds de 17 emplacements a la grandeur de leur aire en utilisant neuf microsatellites, deux sites d'ADN mitochondrial (ADNmt) et de 4918 a 8835 sites de polymorphisme mononucleotidique (SNP). Nos analyses font ressortir une division phylogenetique profonde entre les portions orientale et occidentale de l'aire de repartition, qui indique vraisemblablement des origines remontant a au moins deux refuges glaciaires pleistocenes distincts. A l'echelle regionale, les microsatellites et les SNPs font ressortir des motifs de subdivision congruents, et la structure des populations obtenue concorde avec les previsions basees sur la connectivite hydrologique. Il est etabli que, au sein des Grands Lacs laurentiens, les lacs Huron et Ontario constituent des regions d'interet. La population du lac Huron semble etre une population source contemporaine pour plusieurs autres Grands Lacs, et le lac Ontario renferme un groupe de menominis ronds distinct sur le plan genetique. Dans tous les cas, plusieurs marqueurs genetiques produisent des motifs semblables, mais les SNP offrent une resolution nettement accrue. Nous en concluons que les populations de menominis ronds sont subdivisees a plusieurs echelles importantes pour la comprehension de leur evolution et la planification de leur conservation. [Traduit par la Redaction], Introduction The round whitefish (Salmonidae; Coregoninae; Prosopium cylindraceum) is a widespread species that has become a conservation concern in several regions of North America. In the northeastern United States, several [...]

We studied microsatellite DNA variation in 15 populations of northwestern North American pygmy whitefish (Prosopium coulterii (Eigenmann and Eigenmann, 1892)), an enigmatic freshwater fish thought to be highly fragmented by residency in deep, cold postglacial lakes. Population subdivision (θ) across 10 loci was 0.12 (P < 0.001) across samples, but one western Alaskan population was more divergent than all others (θ = 0.31-0.41, P < 0.001). Within the Williston Reservoir watershed (WRW), θ averaged 0.08 (P < 0.001) and was positively associated with both the geographic distance between localities ([r.sup.2] = 0.36, P < 0.001) and the number of branch points interconnecting them ([r.sup.2] = 0.33, P < 0.001). Differentiation among populations was modeled as the sum of the genetic distances for the stream sections interconnecting them ([r.sup.2] = 0.74). Differences among subwatersheds with the WRW accounted for 5.1% of the total variation in allele frequencies (P < 0.001). Assignment tests suggested limited movement among lakes, with most inferred dispersal between adjacent watersheds. Coalescent analysis strongly supported a gene flow-drift equilibrium model of population structure over a drift-only model. Effective management of diversity in pygmy whitefish requires the maintenance of stream networks that interconnect lakes within a watershed. Nous etudions la variation de l'ADN des microsatellites dans 15 populations du nord-ouest de l'Amerique du Nord du menomini pygmee, Prosopium coulterii (Eigenmann et Eigenmann, 1892), un poisson d'eau douce enigmatique dont on croit les populations fortement fragmentees a cause de leur residence dans des lacs postglaciaires profonds et froids. La subdivision de la population (θ) dans 10 locus est de 0,12 (P < 0,001) dans l'ensemble des echantillons, bien qu'une population de l'ouest de l'Alaska soit plus divergente que toutes les autres (θ = 0,31-0,41, P < 0,001). Dans le bassin hydrographique du reservoir Williston (WRW), θ a une valeur moyenne de 0,08 (P < 0,001) et est en correlation positive tant avec la distance geographique entre les localites ([r.sup.2] = 0,36, P < 0,001) qu'avec le nombre de points de branchement qui les relie ([r.sup.2] = 0,33, P < 0,001). La differentiation entre les populations peut se modeliser comme la somme des distances genetiques des sections de cours d' eau qui les rattachent ([r.sup.2] = 0,74). La differenciation entre les sous-bassins au sein de WRW explique 5,1 % de la variation totale dans la frequence des alleles (P < 0,001). Des tests d'assignation indiquent des deplacements limites entre les lacs, avec la dispersion le plus souvent retrouvee entre des bassins versants adjacents. Une analyse de coalescence appuie fortement un modele de structure de population avec equilibre entre le flux genique et la derive, plutot qu'un modele de derive seule. Une gestion efficace de la diversite chez les menominis pygmees necessite le maintien des reseaux de cours d'eau qui relient les lacs dans un meme bassin versant. [Traduit par la Redaction], Introduction In geographically widespread species, the extent of population subdivision, or the degree to which species are subdivided into at least partially genetically distinct units, will be a function both [...]

We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.). Our goals were to elucidate the genomic distribution and sex specificity of brain expression QTL (eQTL) and to determine the extent to which genes controlling transcriptional variation may underlie adaptive divergence in the recently evolved dwarf(limnetic) and normal (benthic) whitefish. We observed a sex bias in transcriptional genetic architecture, with more eQTL observed in males, as well as divergence in genome location of eQTL between the sexes. Hotspots of nonrandom aggregations of up to 32 eQTL in one location were observed. We identified candidate genes for species pair divergence involved with energetic metabolism, protein synthesis, and neural development on the basis of colocalization of eQTL for these genes with eight previously identified adaptive phenotypic QTL and four previously identified outlier loci from a genome scan in natural populations. Eighty-eight percent of eQTL-phenotypic QTL colocalization involved growth rate and condition factor QTL, two traits central to adaptive divergence between whitefish species pairs. Hotspots colocalized with phenotypic QTL in several cases, revealing possible locations where master regulatory genes, such as a zinc-finger protein in one case, control gene expression directly related to adaptive phenotypic divergence. We observed little evidence of colocalization of brain eQTL with behavioral QTL, which provides insight into the genes identified by behavioral QTL studies. These results extend to the transcriptome level previous work illustrating that selection has shaped recent parallel divergence between dwarf and normal lake whitefish species pairs and that metabolic, more than morphological, differences appear to play a key role in this divergence.

Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied toward investigating the regulation architecture of genes involved in the process of population divergence, ultimately leading to speciation events. Here, we conducted an eQTL mapping experiment to compare the genetic architecture of transcript regulation in adaptive traits, differentiating the recently evolved limnetic (dwarf) and benthic (normal) species pairs of lake whitefish. The eQTL were mapped in three data sets derived from an [F.sub.1] hybriddwarf backcrossed family: the entire set of 66 genotyped individuals and the two sexes treated separately. We identified strikingly more eQTL in the female data set (174), compared to both male (54) and combined (33) data sets. The majority of these genes were not differentially expressed between male and female progeny of the backcross family, thus providing evidence for a strong pleiotropic sex-linked effect in transcriptomic regulation. The subtelomeric region of a linkage group segregating in females encompassed >50% of all eQTL, which exhibited the most pronounced additive effects. We also conducted a direct comparison of transcriptomic profiles between pure dwarf and normal progeny reared in controlled conditions. We detected 34 differentially expressed transcripts associated with eQTL segregating only in sexspecific data sets and mostly belonging to functional groups that differentiate dwarf and normal whitefish in natural populations. Therefore, these eQTL are not related to interindividual variation, but instead to the adaptive and historical genetic divergence between dwarf and normal whitefish. This study exemplifies how the integration of genetic and transcriptomic data offers a strong means for dissecting the functional genomic response to selection by separating mapping family-specific effects from genetic factors under selection, potentially involved in the phenotypic divergence of natural populations.

Body composition traits have potential use in fish breeding programs as indicator traits for selective improvement of feed efficiency. Moreover, feed companies are increasingly replacing traditional fish meal (FM) based ingredients in feeds for carnivorous farmed fish with plant protein ingredients. Therefore, genetic relationships of composition and feed utilization traits need to be quantified for both current FM-based and future plant-based aquaculture feeds. Individual whole-body lipid% and protein%, daily gain (DG), ADFI, and G:F (daily gain/daily feed intake) were measured on 1,505 European whitefish (Coregonus lavaretus) from 70 half/full-sib families reared in a split-family design with either a typical FM or a novel soybean meal (SBM) based diet. Diet-specific genetic parameters were estimated with multiple-trait animal models. Lipid% was significantly greater in the FM diet group than in the SBM group, even independent of final BW or total feed intake. In both diets, lipid% showed moderate heritability (0.12 to 0.22) and had positive phenotypic and genetic correlations with DG (0.37 to 0.82) and ADFI (0.36 to 0.88). Therefore, selection against lipid% can be used to indirectly select for lower feed intake. Protein% showed low heritability (0.05 to 0.07), and generally very weak or zero correlations with DG and ADFI. In contrast to many previous studies on terrestrial livestock, lipid% showed zero or very weak phenotypic and genetic correlations with G:F. However, selection index calculations demonstrated that simultaneous selection for high DG and reduced lipid% could be used to indirectly increase G:F; this strategy increased absolute genetic response in G:F by a factor of 1.5 to 1.6 compared with selection on DG alone. Lipid% and protein% were not greatly affected by genotype-diet environment interactions, and therefore, selection strategies for improving body composition within current FM diets should also improve populations for future SBM diets. Key words: feed efficiency, genetic selection, genotype-environment interaction, lipid, protein

Correlated trophic specialization and genetic divergence have been studied in sympatric lake whitefish ecotypes (Coregonus clupeaformis) with focus on the ecological speciation hypothesis. Analysis of morphological differentiation between dwarf and normal whitefish ecotypes has been extended into six lakes and compared to the extent of genetic differentiation assessed at microsatellite loci. Negative correlation, which constitutes support for the hypothesis, was seen between extent of morphological differentiation related to trophic-related traits and that of between-ecotype gene flow in different lakes.

The SinaI family of repeats is present only in the chum salmon and the pink salmon, and it is not present in five other species in the same genus or in other species in closely related genera. In the present study, we showed that another short interspersed repetitive elements (SINEs) family, which is almost identical to the Sinai family, is present in all fishes in the subfamily Coregoninae, being regarded as the most primitive salmonids. This new family of SINEs was designated the SmaI-cor family (SmaI family of repeats in coregonids). The consensus sequence of the SmaI-cor family was found to be 98.6% homologous to that of the Sinai family. Accordingly, it is difficult to explain the high degree of homology between these two families of SINEs by any mechanism other than the horizontal transfer of SINEs. The estimates of the rate of neutral mutation of nuclear genes, comparing chum salmon and European whitefish, confirmed this possibility. Our results strongly suggest that a member(s) of the SmaI-cor family might have been transferred horizontally from one coregonid species to a common ancestor of chum and pink salmon or to these two species independently, to allow subsequent amplification of the SmaI family in their respective genomes.

A query that whether ectoparasitic Argulus coregoni egg hatchin pattern can be explained as a generically canalized individual trait, an instance of phenotypic plasticity or bet-hedging is focused. In order to clear this concept, egg clutches laid by individual A. coregoni females in early and late reproductive period of lice population were collected and clutches were randomized within 3 treatments.

The white fish species 'Chirostoma estor, C. humboldtianum, C. lucius, C. promelas' and 'C. sphyraena' are of great economical, ichtyological and ecological relevance to the local populations of Patzcuaro and Chapala lakes, Mexico. Several aquaculture programs had recently started in these regions in order to provide high quality food, however the genetic identities or morphological characters used to discriminate among these species and for practical purposes are uncertain. The species are part of the Jordani group (Barbour 1973 a) and are characterized by their high genetic identities and morphology (Barbour 1973 a y b; Barbour y Chernoff 1984; Echelle y Echelle 1984; Barriga-Sosa et al., 2002; Barriga-Sosa 2001). Here we present the preliminary results of 490 bp and 600 bp of the mtDNA cytocrome B and 16S DNA genes, respectively. The mean aligned identity of the compiled sequences and in relation to other teleost fish were 79.8 and 88.6% for cytochrome B and 16S DNA, respectively. The number of variable sites among the species analyzed and for the cyt B was 1.7% (in 423 bp), whereas for the 16S DNA gene it was 3.3%, as well as 23 insertions. An RFLP analysis of the 16S DNA amplified and sequenced fragment and with the enzymes Ava II, Hae III, Ndel, Taq I and Mnl I showed that these species can be practically discriminated for aquaculture practices.