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

Benavente, Javiera N. / Véliz, David / Quezada‐Romegialli, Claudio / Gomez‐Uchida, Daniel

Journal of Fish Biology. 2023 Dec., v. 103, no. 6 p.1277-1288

2023

Abstract: 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, ...

Abstract	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.
Keywords	Biological Sciences ; Oncorhynchus mykiss ; aquaculture ; biodiversity ; breeding stock ; genetic structure ; genetic variation ; genotyping ; haplotypes ; trout ; Andes region ; Argentina ; Chile ; Europe ; North America
Language	English
Dates of publication	2023-12
Size	p. 1277-1288.
Publishing place	Blackwell Publishing Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	410564-3
ISSN	1095-8649 ; 0022-1112
ISSN (online)	1095-8649
ISSN	0022-1112
DOI	10.1111/jfb.15520
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Biomarker selection depends on gene function and organ: the case of the cytochrome P450 family genes in freshwater fish exposed to chronic pollution.

Cortés-Miranda, Jorge / Rojas-Hernández, Noemí / Muñoz, Gigliola / Copaja, Sylvia / Quezada-Romegialli, Claudio / Veliz, David / Vega-Retter, Caren

PeerJ

2024 Volume 12, Page(s) e16925

Abstract: Pollution and its effects have been of major concern in recent decades. Many strategies and markers have been developed to assess their effects on biota. Cytochrome P450 (CYP) genes have received significant attention in this context because of their ... ...

Abstract	Pollution and its effects have been of major concern in recent decades. Many strategies and markers have been developed to assess their effects on biota. Cytochrome P450 (CYP) genes have received significant attention in this context because of their relationship with detoxification and activation of exogenous compounds. While their expression has been identified as a pollution exposure biomarker, in most cases, it has been tested only after acute exposures and for CYP genes associated with exogenous compounds. To elucidate CYP gene expression patterns under chronic pollution exposure, we have used the silverside
MeSH term(s)	Animals ; Fishes/genetics ; Cytochrome P-450 Enzyme System/genetics ; Environmental Pollution ; Biomarkers ; Fresh Water
Chemical Substances	Cytochrome P-450 Enzyme System (9035-51-2) ; Biomarkers
Language	English
Publishing date	2024-02-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359 ; 2167-8359
ISSN (online)	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.16925
Database	MEDical Literature Analysis and Retrieval System OnLINE

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

Benavente, Javiera N / Véliz, David / Quezada-Romegialli, Claudio / Gomez-Uchida, Daniel

Journal of fish biology

2023 Volume 103, Issue 6, Page(s) 1277–1288

Abstract	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.
MeSH term(s)	Animals ; Oncorhynchus mykiss/genetics ; Polymorphism, Single Nucleotide ; Genetic Structures ; DNA, Mitochondrial/genetics ; Chile
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2023-09-05
Publishing country	England
Document type	Journal Article
ZDB-ID	410564-3
ISSN	1095-8649 ; 0022-1112
ISSN (online)	1095-8649
ISSN	0022-1112
DOI	10.1111/jfb.15520
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Understanding morphological variability in a taxonomic context in Chilean diplomystids (Teleostei: Siluriformes), including the description of a new species.

Arratia, Gloria / Quezada-Romegialli, Claudio

PeerJ

2017 Volume 5, Page(s) e2991

Abstract: Following study of the external morphology and its unmatched variability throughout ontogeny and a re-examination of selected morphological characters based on many specimens of diplomystids from Central and South Chile, we revised and emended previous ... ...

Abstract	Following study of the external morphology and its unmatched variability throughout ontogeny and a re-examination of selected morphological characters based on many specimens of diplomystids from Central and South Chile, we revised and emended previous specific diagnoses and consider
Language	English
Publishing date	2017-02-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.2991
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Next generation sequencing yields the complete mitochondrial genome of the Endangered Chilean silverside Basilichthys microlepidotus (Jenyns, 1841) (Teleostei, Atherinopsidae), validated with RNA-seq.

Véliz, David / Vega-Retter, Caren / Quezada-Romegialli, Claudio

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis

2016 Volume 27, Issue 2, Page(s) 1505–1506

Abstract: The complete sequence of the mitochondrial genome for the Chilean silverside Basilichthys microlepidotus is reported for the first time. The entire mitochondrial genome was 16,544 bp in length (GenBank accession no. KM245937); gene composition and ... ...

Abstract	The complete sequence of the mitochondrial genome for the Chilean silverside Basilichthys microlepidotus is reported for the first time. The entire mitochondrial genome was 16,544 bp in length (GenBank accession no. KM245937); gene composition and arrangement was conformed to that reported for most fishes and contained the typical structure of 2 rRNAs, 13 protein-coding genes, 22 tRNAs and a non-coding region. The assembled mitogenome was validated against sequences of COI and Control Region previously sequenced in our lab, functional genes from RNA-Seq data for the same species and the mitogenome of two other atherinopsid species available in Genbank.
MeSH term(s)	Animals ; Base Composition ; Endangered Species ; Fishes/genetics ; Gene Order ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods
Language	English
Publishing date	2016
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2470-1408
ISSN (online)	2470-1408
DOI	10.3109/19401736.2014.953113
Database	MEDical Literature Analysis and Retrieval System OnLINE

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

Prida, Valentina / Sepúlveda, Maritza / Quezada-Romegialli, Claudio / Harrod, Chris / Gomez-Uchida, Daniel / Cid, Beatriz / Canales-Aguirre, Cristian B

Foods (Basel, Switzerland)

2020 Volume 9, Issue 11

Abstract: Species diagnosis is essential to assess the level of mislabeling or misnamed seafood products such as sushi. In Chile, sushi typically includes salmon as the main ingredient, but species used are rarely declared on the menu. In order to identify which ... ...

Abstract	Species diagnosis is essential to assess the level of mislabeling or misnamed seafood products such as sushi. In Chile, sushi typically includes salmon as the main ingredient, but species used are rarely declared on the menu. In order to identify which species are included in the Chilean sushi market, we analyzed 84 individual sushi rolls sold as "salmon" from sushi outlets in ten cities across Chile. Using a polymerase chain reaction-restriction fragment length polymorphism protocol (PCR-RFLP), we identified mislabeled and misnamed products. Atlantic salmon was the most common salmonid fish used in sushi, followed by coho salmon, rainbow trout, and Chinook salmon. We found a total of 23% and 18% of the products were mislabeled and misnamed, respectively. In 64% of cases, the salesperson selling the product could not identify the species. We also identified the use of wild-captured Chinook salmon samples from a naturalized population. Our results provide a first indication regarding species composition in Chilean sushi, a quantification of mislabeling and the level of misinformation declared by sales people to consumers. Finally, considering that Chinook salmon likely originates from a non-licensed origin and that sushi is an uncooked product, proper identification in the food production chain may have important consequences for the health of consumers.
Language	English
Publishing date	2020-11-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704223-6
ISSN	2304-8158
ISSN	2304-8158
DOI	10.3390/foods9111699
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The complete mitochondrial genome of the rocky reef fish Cheilodactylus variegatus Valenciennes, 1833 (Teleostei: Cheilodactylidae).

Quezada-Romegialli, Claudio / Véliz, David / Docmac, Felipe / Harrod, Chris

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis

2016 Volume 27, Issue 4, Page(s) 2359–2360

Abstract: Cheilodactylus variegatus is a common benthivorous marine fish inhabiting in rocky subtidal habitats in the eastern south Pacific coast of Chile and Peru. However, its biology and ecology are relatively understudied and its taxonomic assignment has been ... ...

Abstract	Cheilodactylus variegatus is a common benthivorous marine fish inhabiting in rocky subtidal habitats in the eastern south Pacific coast of Chile and Peru. However, its biology and ecology are relatively understudied and its taxonomic assignment has been debated recently. The complete mitochondrial genome was assembled de novo and mapped to a reference using 5.97 million of reads obtained through Ion Torrent next generation sequencing, resulting in a circular sequence of 16,652 bp in length. Gene composition and arrangement comprised to that reported for most fishes and contained the typical structure of 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 1 non-coding region. This mitogenome provides a valuable resource for studies of fish molecular systematics, phylogeography and population genetics.
Language	English
Publishing date	2016-07
Publishing country	England
Document type	Journal Article
ISSN	2470-1408
ISSN (online)	2470-1408
DOI	10.3109/19401736.2015.1025263
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The complete mitochondrial genome of the endemic and threatened killifish Orestias ascotanensis Parenti, 1984 (Cyprinodontiformes, Cyprinodontidae) from the High Andes.

Quezada-Romegialli, Claudio / Guerrero, Claudia Jimena / Véliz, David / Vila, Irma

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis

2016 Volume 27, Issue 4, Page(s) 2798–2799

Abstract: The killifish Orestias ascotanensis is endemic to the small isolated springs of Ascotán salt pan in the Central High Andes, Chile. Due to small populations, mining activity, and increasing aridity, this species is catalogued in danger of extinction. The ... ...

Abstract	The killifish Orestias ascotanensis is endemic to the small isolated springs of Ascotán salt pan in the Central High Andes, Chile. Due to small populations, mining activity, and increasing aridity, this species is catalogued in danger of extinction. The complete mitochondrial genome of O. ascotanesis was assembled with an Ion Torrent sequencer (chip 318) that produced 2.61 million of reads. The 16 617 bp of the entire genome consisted of 22 transfer RNAs, 2 ribosomal RNAs, 13 protein-coding genes, and a control region, showing that the gene composition and arrangement match to that reported for most fishes.
Language	English
Publishing date	2016-07
Publishing country	England
Document type	Journal Article
ISSN	2470-1408
ISSN (online)	2470-1408
DOI	10.3109/19401736.2015.1053072
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The complete mitochondrial genome of the killifish Orestias sp. (Cyprinodontiformes, Cyprinodontidae) from the high Andean range.

Quezada-Romegialli, Claudio / Guerrero, Claudia Jimena / Véliz, David / Vila, Irma

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis

2016 Volume 27, Issue 4, Page(s) 2840–2841

Abstract: The killifish genus Orestias is endemic to freshwater ecosystems in the High Andes of Peru, Bolivia and Chile. Phylogenetic and phylogeographic studies with partial mitochondrial genes have failed to resolve relationship among species, needing more ... ...

Abstract	The killifish genus Orestias is endemic to freshwater ecosystems in the High Andes of Peru, Bolivia and Chile. Phylogenetic and phylogeographic studies with partial mitochondrial genes have failed to resolve relationship among species, needing more comprehensive approaches. In this study, we described the complete mitochondrial genome of Orestias sp. from Lirima, northern Chile, with the aim to provide useful data for phylogenetic purposes and species delimitation. The mitochondrial genome was assembled with 2.6 million of reads obtained through an Ion Torrent (chip 318) sequencer. The circular sequence of 16,617 bp showed the following nucleotide composition: A, 26.7%, C, 27.1%, G, 17.0%, and T, 29.2%. Gene composition and structure were similar to other fish sequences available, and comprised 13 protein-coding genes, 12S and 16S rRNA, 22 tRNA genes, and a control region.
Language	English
Publishing date	2016-07
Publishing country	England
Document type	Journal Article
ISSN	2470-1408
ISSN (online)	2470-1408
DOI	10.3109/19401736.2015.1053119
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Morphological and taxonomic descriptions of a new genus and species of killifishes (Teleostei: Cyprinodontiformes) from the high Andes of northern Chile.

Arratia, Gloria / Vila, Irma / Lam, Natalia / Guerrero, Claudia Jimena / Quezada-Romegialli, Claudio

PloS one

2017 Volume 12, Issue 8, Page(s) e0181989

Abstract: A new genus and species, Pseudorestias lirimensis, is described from the southern part of the Chilean Altiplano. While sharing several characters that clearly align the new species with Orestias, this new fish is characterized by numerous autapomorphies: ...

Abstract	A new genus and species, Pseudorestias lirimensis, is described from the southern part of the Chilean Altiplano. While sharing several characters that clearly align the new species with Orestias, this new fish is characterized by numerous autapomorphies: the Meckel cartilage is a continuous cartilage that broadly expands posteriorly (in large specimens, it keeps its anterior part and is resorbed posteriorly), the basibranchials are fused into one long element, the second pharyngobranchial is not displaced dorsally over pharyngobranchial tooth plate 3+4, but they are aligned, the anterior and posterior ceratohyals are closely articulated keeping a scarce amount of cartilage between both bones and ventral to them, ossified middle and distal dorsal radials are present in females as well as ossified middle and distal anal radials. Pseudorestias lirimensis presents strong sexual dimorphism associated to size. Females are almost twice as large and long than males, neuromast lines are absent in males, a mesethmoid is present in males, squamation on head is reduced in males, and ossified middle and distal radial of dorsal fin are cartilaginous in males. Pseudorestias and Orestias are suggested as the sole members of the tribe Orestiini. A list of characters diagnosing the tribe is provided. The presence of the new genus is interpreted as a possible result of the ecosystem isolation where the fish is living from surrounding basins-as early as possibly from the Miocene-Pliocene times-and its physical and chemical characteristics. Small populations, living conditions, small habitat, and reduced distribution make this species a strong candidate to be considered critically endangered, a situation already established for all other Chilean species living in the Altiplano. There is high probability it will become extinct due to water demands and climate change in the region.
MeSH term(s)	Animals ; Chile ; Chromosomes ; Classification ; DNA, Mitochondrial ; Ecosystem ; Endangered Species ; Female ; Killifishes/anatomy & histology ; Killifishes/genetics ; Lakes ; Male ; Reproductive Isolation ; Sex Characteristics
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2017-08-08
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0181989
Database	MEDical Literature Analysis and Retrieval System OnLINE

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