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

Abstract

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.

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

“…Biparental SNPs indicated that the contemporary genetic structure of rainbow trout appeared influenced by natural causes, via the presence of divergent populations with related individuals in isolated sites, and by anthropogenic causes, via the presence of admixed populations in sites affected by commercial aquaculture as well as human‐mediated dispersal. These have likely shaped the genetic diversity of rainbow trout inhabiting multiple locations in Chile as seen in previous studies (Canales‐Aguirre et al, 2018; Carcamo et al, 2015; Colihueque et al, 2019; Consuegra et al, 2011).…”

“…Rainbow trout have been extensively studied at both genetic and genomic levels. mtDNA sequences have been used to study phylogeographic patterns of the species in its native range (Brunelli et al, 2010; Graziano et al, 2005; Nielsen, 1999; Nielsen et al, 1998) and find the origin of introduced populations (Colihueque et al, 2019; Stanković et al, 2016). More recently, SNPs have been used for population genetic studies in both native (Fraik et al, 2021; Kelson et al, 2020; Limborg et al, 2012) and introduced ranges (Benavente et al, 2015; Canales‐Aguirre et al, 2018).…”

“…Colihueque et al (2019) used another segment of the mtDNA control region to correlate the presence of two different haplotype lineages in rivers of southern…”

Environmental risk assessment of non‐native salmonid escapes from net pens in the Chilean Patagonia

“…From the three farmed species, rainbow trout is the only species showing widespread naturalization and very high invasion capacity, 29,30,77 which is a relevant consideration despite its low representation in the salmon farming production (Figure 1). Also, risks associated with escapes of this species could be higher than anticipated because farmed trout have been selected for faster growth and resiliency 78 .…”

Chilean Salmon Sushi: Genetics Reveals Product Mislabeling and a Lack of Reliable Information at the Point of Sale

“…Although the bulk of Chile's salmonid production is exported, these three cultured species can also be sold nationally following statutory requirements [9]. In addition to aquaculture fish, Chile also supports widespread and abundant populations of naturalized salmonid fishes, where the entire life cycle is completed as free-living individuals [10] including rainbow trout, Chinook salmon (Oncorhynchus tshawytscha), and brown trout (Salmo trutta) [11][12][13][14]. There is evidence that such naturalized populations could make significant contributions to commercial services supporting human consumption (e.g., Chinook salmon), but the scale or geographical distribution of services for these species provide is unclear.…”