Deep divergence and apparent sex-biased dispersal revealed by a Y-linked marker in rainbow trout

Uniparental and biparental markers unravel invasion pathways, population admixture, and genetic structure in naturalized rainbow trout (Oncorhynchus mykiss)

The present study combined uniparental mtDNA and biparental SNPs to illuminate the invasion and colonization pathways of rainbow trout, Oncorhynchus mykiss, one of the world's most widespread invasive fishes, that has been intensively propagated in Chile, South America. The specific aims of the study were (i) to evaluate potential donor populations, which could be either from the species' native range in North America or from introduced populations in Europe, by comparing mtDNA D-loop/control region haplotypes; and (ii) to assess the factors that have shaped genetic diversity and contemporary genetic structure of rainbow trout populations introduced to Chile through SNP genotyping. The authors comprehensively sampled 24 sites in 12 basins ranging from the High Andean Plateau (Altiplano, 18° S) to northern Patagonia (41° S). Results of the mtDNA data of naturalized trout populations from rivers in the Altiplano (northern Chile) differed from those collected in central and southern Chile, suggesting an origin from North American hatcheries. Naturalized trout populations in central and southern Chile, on the contrary, shared haplotypes with specimens found in European hatcheries. The southern and central Chile populations also contained rare haplotypes, possibly indicating potential spread through aquaculture escapes. Results of the SNP analysis revealed higher allelic richness for trout sampled in sites influenced by commercial aquaculture than sites without commercial aquaculture, likely due to increased admixture between aquaculture broodstock and naturalized trout. The analysis further uncovered some complex patterns of divergent trout populations with low genetic diversity as well as increased relatedness between individuals from isolated sites, suggesting possible local populations. A comprehensive characterization of genetic diversity and structure of rainbow trout should help identify management areas that may augment socioeconomic benefits while preventing the spread and further impacts on biodiversity.

Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding

Genetic diversity underpins species conservation and management goals, and ultimately determines a species' ability to adapt. Using freshwater environmental DNA (eDNA) samples, we examined mitochondrial genetic diversity using multigene metabarcode sequence data from four Oncorhynchus species across 16 sites in Oregon and northern California. Our multigene metabarcode panel included targets commonly used in population genetic NADH dehydrogenase 2 (ND2), phylogenetic cytochrome c oxidase subunit 1 (COI) and eDNA (12S ribosomal DNA) screening. The ND2 locus showed the greatest within-species haplotype diversity for all species, followed by COI and then 12S rDNA for all species except Oncorhynchus kisutch. Sequences recovered for O. clarkii clarkii were either identical to, or one mutation different from, previously characterized haplotypes (95.3% and 4.5% of reads, respectively). The greatest diversity in O. c. clarkii was among coastal watersheds, and subsets of this diversity were shared with fish in inland watersheds. However, coastal streams and the Umpqua River watershed appear to harbour unique haplotypes. Sequences from O. mykiss revealed a disjunction between the Willamette watershed and southern watersheds suggesting divergent histories. We also identified similarities between populations in the northern Deschutes and southern Klamath watersheds, consistent with previously hypothesized connections between the two via inland basins. Oncorhynchus kisutch was only identified in coastal streams and the Klamath River watershed, with most diversity concentrated in the coastal Coquille watershed. Oncorhynchus tshawytscha was only observed at one site, but contained multiple haplotypes at each locus. The characterization of genetic diversity at multiple loci expands the knowledge gained from eDNA sampling and provides crucial information for conservation actions and genetic management.

Sex identification of the ornamental amazon fish Astronotus ocellatus by videoceloscopy and gonadal biopsy

This study was conducted to evaluate and validate the efficacy and safety of videoceloscopy and gonadal biopsy as sexing methods for the A. ocellatus. A total of 31 adult individuals were used. Florfenicol (50 mg/kg) and morphine (5 mg/kg) were administered intramuscularly during the pre-surgical period. Animals were maintained in a supine position preceding a ventral midline incision and endoscope optics were then utilized for gonad visualization and sex identification. A gonadal fragment was collected using laparoscopic forceps and conditioned in 10 % formalin. To suture the cavity, polyamide yarn was used in a simple and continuous pattern. At 15 days subsequent to surgery, healing was evaluated, and the stitches were removed. Videoceloscopy accuracy and gonadal biopsy effectiveness were 97 % and 83 %, respectively. Total time devoted in the videoceloscopy, gonadal biopsy and surgery was longer for animals identified as males compared to females The survival rate was 100 %. There were differences regarding food consumption at 24 and 36 h post-surgery when compared to control specimens (pre-surgical) Regarding position in the water column, differences were observed at 24 and 72 h after surgery when compared individually to the control specimens. There were differences for interaction behavior at 24, 36 and 60 h, and regarding search for hiding places at 12 and 24 h after surgery in relation to the control specimens. The applied videoceloscopy and gonadal biopsy surgical techniques are, therefore, effective and safe for A. ocellatus sexing procedures.

Genetic Differentiation and Origin of Naturalized Rainbow Trout Populations From Southern Chile, Revealed by the mtDNA Control Region Marker

Numerous self-sustaining naturalized or introduced populations of rainbow trout (Oncorhynchus mykiss) are widely distributed throughout the freshwaters of southern Chile. In this study, analysis of the mitochondrial DNA control region (CR) marker was conducted to investigate the level of genetic divergence among populations and their phylogenetic relationships with respect to native lineages. This information provided a framework to interpret the genetic structure and origin that was shaped during historical trout introduction efforts. To this end, we analyzed eleven naturalized populations of lakes and rivers from five basins. The CR marker revealed five haplotypes. The overall haplotype (H) and nucleotide (Π) diversities were 0.684 ± 0.030 and 0.00460 ± 0.00012, respectively. Global F_ST was 0.169, with several pairwise F_ST estimates showing significant differences (P < 0.05). The exact test of population differentiation corroborated this result (P < 0.001). Significant geographic structure was found (P < 0.05), with variations explained primarily by differences within populations (61.65%) and among group basins (20.82%). Maximum likelihood phylogenetic analysis resolved two distinct clades with medium bootstrap support when naturalized populations were aligned in conjunction with reference native lineages. The haplotype network revealed a close association between naturalized populations and four main haplotypes representative of three native ecotypes or lineages from western North America (rainbow trout, steelhead trout and redband trout). These results indicate a genetic population structuring for naturalized rainbow trout from southern Chile and an origin probably represented by multiple lineages sources. Thus, mitochondrial DNA data strongly suggest that stocking of rainbow trout from different origins may have occurred during or after the initial introduction efforts.

The Adaptive Sex in Stressful Environments

The impact of early stress on juvenile development has intrigued scientists for decades, but the adaptive significance of such effects remains an ongoing debate. This debate has largely ignored some characteristics of the offspring, such as their sex, despite strong evolutionary and demographic implications of sex-ratio variation. We review recent studies that examine associations between glucocorticoids (GCs), the main class of stress hormones, and offspring sex. Whereas exposure to GCs at around the time of sex determination in fish consistently produces males, the extent and direction of sex-ratio bias in response to stress vary in reptiles, birds, and mammals. We propose proximate and ultimate explanations for most of these trends.

Y chromosome phylogeny for cutthroat trout (Oncorhynchus clarkii) subspecies is generally concordant with those of other markers

Sequence divergence was evaluated in the non-recombining, male-specific OmyY1 region of the Y chromosome among the subspecies of cutthroat trout (Oncorhynchus clarkii) in the western United States. This evaluation identified subspecies-discriminating OmyY1-haplotypes within a ∼1200bp region of the OmyY1 locus and localized the region to the end of the Y chromosome by FISH analysis. OmyY1 sequences were aligned and used to reconstruct a phylogeny of the cutthroat trout subspecies and related species via maximum-parsimony and Bayesian analyses. In the Y-haplotype phylogeny, clade distributions generally corresponded to the geographic distributions of the recognized subspecies. This phylogeny generally corresponded to a mitochondrial tree obtained for these subspecies in a previous study. Both support a clade of trout vs. Pacific salmon, of rainbow trout, and of a Yellowstone cutthroat group within the cutthroat trout. In our OmyY1 tree, however, the cutthroat "clade", although present topologically, was not statistically significant. Some key differences were found between trees obtained from the paternally-inherited OmyY1 vs. maternally-inherited mitochondrial haplotypes in cutthroat trout compared to rainbow trout. Other findings are: The trout OmyY1 region evolves between 3 and 13 times slower than the trout mitochondrial regions that have been studied. The Lahontan cutthroat trout had a fixed OmyY1 sequence throughout ten separate populations, suggesting this subspecies underwent a severe population bottleneck prior to its current dispersal throughout the Great Basin during the pluvial phase of the last ice age. The Yellowstone group is the most derived among the cutthroat trout and consists of the Yellowstone, Bonneville, Colorado, Rio Grande and greenback subspecies. Identification of subspecies and sex with this Y-chromosome marker may prove useful in conservation efforts.

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

Salmonid fishes exhibit extensive local adaptations owing to abundant environmental variation and precise natal homing. This extensive local adaptation makes conservation and restoration of salmonids a challenge. For example, defining unambiguous units of conservation is difficult, and restoration attempts often fail owing to inadequate adaptive matching of translocated populations. A better understanding of the genetic architecture of local adaptation in salmonids could provide valuable information to assist in conserving and restoring natural populations of these important species. Here, we use a combination of laboratory crosses and next-generation sequencing to investigate the genetic architecture of the parallel adaptation of rapid development rate in two geographically and genetically distant populations of rainbow trout (Oncorhynchus mykiss). Strikingly, we find that not only is a parallel genetic mechanism used but that a conserved haplotype is responsible for this intriguing adaptation. The repeated use of adaptive genetic variation across distant geographical areas could be a general theme in salmonids and have important implications for conservation and restoration.

Molecular sexing and population genetic inference using a sex-linked microsatellite marker in the nine-spined stickleback (Pungitius pungitius)

BACKGROUND

Sex-specific DNA markers can serve as tools for molecular sex identification, as well as for population genetic inferences. We investigated the potential utility of a microsatellite marker located on sex chromosomes for molecular sexing of Fennoscandian nine-spined sticklebacks (Pungitius pungitius). In addition, we assessed the patterns of allelic differentiation between X and Y chromosomes across the populations to examine if the sex chromosomes had been highly differentiated prior to the postglacial recolonization of Fennoscandia.

FINDINGS

A clear and consistent sex difference in allele size distribution was observed at the Stn19 locus throughout the 15 populations investigated. Males were distinguishable by the presence of distinct male-specific alleles, which were lacking in all females. There was no indication of recombination between sex and the Stn19 locus in the 647 individuals tested. The degree of genetic differentiation between the X and Y chromosomes was much higher than that of interpopulation differentiation in the respective chromosomes.

CONCLUSIONS

Our results indicate that the Stn19 locus can be used for molecular sex identification in Fennoscandian nine-spined sticklebacks. The consistent pattern of high allelic differentiation between the X and Y chromosomes in these populations suggests that the sex chromosomes were already highly differentiated prior to the postglacial recolonization of Fennoscandia.