Daniel Gomez-Uchida

University of Concepción · Departamento de Zoología

Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor an important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently in...

Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently inves...

Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently inves...

Marine derived nutrients (MDN) contained in gametes (mature eggs and sperm), carcasses and metabolic wastes from anadromous migratory salmon can transfer energy and materials to fresh water, thereby affecting the structure and function of stream ecosystems. This is crucial among ecosystems where humans have mediated biological invasions by propagat...

Here, we review extensive information to estimate environmental risks from escaped non‐native salmonids based on the assessments of hazard, sensitivity and exposure of discrete water bodies in Chile. In 2020, the country harvested about 1 million tons salmonids from net pens located along 1500 km of highly biodiverse coastline. We base our analysis...

The Neotropical region hosts 4,225 freshwater fish species, ranking first among the world’s most diverse regions for freshwater fishes. Our NEOTROPICAL FRESHWATER FISHES data set is the first to produce a large-scale Neotropical freshwater fish inventory, covering the entire Neotropical region from Mexico and the Caribbean in the north, to the sout...

Limited stocking efforts to introduce Atlantic salmon Salmo salar into Chilean rivers and streams were unsuccessful during the 20 th century. Following the arrival of the aquaculture industry during the 1980s, escaped Atlantic salmon have presented an ecological risk to native taxa through predation, competition, and transmission of pathogens or pa...

Since the last decade, the Chinook salmon has become an invasive species in southern Chilean rivers, affecting their environment and displacing native species due to predation and competition. The socioeconomic valuation of this species is complex, due to its high economic, touristic, and culinary value. The tourism industry and artisanal fishing g...

Ecological interactions among multiple invaders can aggravate their effects on invaded systems. Many salmonids including rainbow trout Oncorhynchus mykiss and Chinook salmon O. tshawytscha have established naturalized populations and co-occur in rivers worldwide. Predation of eggs and juveniles has been well documented among salmonids in their nati...

Thouarella Gray, 1870, is one of the most speciose genera among gorgonians of the family Primnoidae (Cnidaria : Octocorallia : Anthozoa), being remarkably diverse in the Antarctic and sub-Antarctic seafloor. However, their diversity in the Southern Ocean is likely underestimated. Phylogenetic analyses of mitochondrial and nuclear DNA markers were i...

We studied how the South American sea lion (SASL, Otaria flavescens ) interacts with the operation of an artisanal fishery of Chinook salmon, a non-native species in Chile, using a combination of biological and social approaches, including a valuation by fishers about this interaction. During austral summer of 2019, an observer onboard artisanal fi...

Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commer...

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 "...

Invasive species with migratory behavior and complex life cycles represent a challenge for evaluating natal sites among individuals. Private and government-sponsored initiatives resulted in the successful introduction and naturalization of Chinook salmon (Oncorhynchus tshawytscha) throughout northern and southern Patagonia in South America. Migrato...

Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, sign...

Thouarella Gray, 1870, is one of the most speciose genera among primnoid gorgonians. It has a worldwide distribution that includes Antarctic and sub-Antarctic regions. Based on a combination of detailed morphological studies and analyses using mitochondrial and nuclear DNA markers, we describe and illustrate three new species of bottlebrush-shaped...

The Cape Horn Biosphere Reserve, one of the last wild areas of the planet, is not exempt from the pressures of global change, such as non‐native species introductions. During 2018 and 2019 we studied the Róbalo river basin in order to update the diversity and distribution of fishes. Here, we report for the first time the native and endangered “Pela...

Chinook salmon are widely distributed across the globe with native stocks in the North Pacific Ocean and self-sustained populations in both the Northern and Southern Hemispheres. In their native range, Chinook salmon face many conservation and management challenges including depleted stocks, loss of genetic diversity, and hatchery influences, where...

El salmón Chinook ha llegado a ser considerado una invasión biológica en ríos del sur de Chile, afectando su entorno ambiental, predando y compitiendo con especies nativas. Pero, a su vez, tiene una apreciación socioeconómica compleja, debido a su alto valor económico, turístico y culinario. La falta de información y reglas hacia la explotación de...

The present review provides an in-depth look into the complex topic of delimiting species in sea anemones. For most part of history this has been based on a small number of variable anatomic traits, many of which are used indistinctly across multiple taxonomic ranks. Early attempts to classify this group succeeded to comprise much of the diversity...

Nile tilapia (Oreochromis niloticus Linnaeus, 1758) belong to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs in this species began in the late 1980s to enhance some traits of commercial interest. The resulting domestication process of Nile tilapia m...

Invasive species with migratory behavior and complex life cycle represent a challenge for evaluating natal sites among individuals. Private and government-sponsored initiatives resulted in the successful introduction and naturalization of Chinook salmon (Oncorhynchus tshawytscha) throughout northern and southern Patagonia in South America. These mi...

The vicuña (Vicugna vicugna) is the most representative wild ungulate of the high Andes of South America with two recognized morphological subspecies, V. v. mensalis in the north and V. v. vicugna in the south of its distribution. Current vicuña population size (460,000-520,000 animals) is the result of population recovery programs established in r...

Chinook salmon (Oticorhynchus tshawytscha Walbaum, 1792) was naturalised in many river systems from South America following aggressive introduction efforts. This study investigated the health status and bacterial diversity of Chinook salmon from the Tolten River in southern Chile. Ribosomal and gene-coding markers were sequenced to establish the pr...

The Southern elephant seal (SES) is a marine species that can be found at sea throughout the Southern Ocean on most sub-Antarctic islands. An unusual record of a solitary Southern elephant seal (Mirounga leonina) in freshwater habitat is reported. The seal was found 16 km upstream from the mouth of the Toltén River, in southern Chile (39°9’S; 73°10...

Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non‐native populations. Yet, our understanding of how artificial (human‐mediated) and natural dispersal pathways of non‐native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the wide...

The phylogenetic resolution provided by genome-wide data has demonstrated the usefulness of RAD sequencing to tackle long-standing taxonomic questions. Cnidarians have recently become a model group in this regard, yet species delimitation analyses have been mostly performed in octocorals. In this study, we used RAD sequencing to test the species hy...

Different pathways of propagation and dispersal of non-native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setti...

We used amplicon sequencing of the 16S rRNA gene to characterize the diversity and assess temporal and spatial patterns of Actinobacteria operational taxonomic units (OTUs) extracted from sediments of the Humboldt Sulfuretum located off the coast of central Chile. The sediment of this zone is rich in sulfur compounds and organic material and suppor...

Knowledge about the genetic underpinnings of invasions-a theme addressed by invasion genetics as a discipline-is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia's freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykis...

Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create...

Pervasive introductions of non-native taxa are behind processes of homogenization of various types affecting the global flora and fauna. Chile’s freshwater ecosystems encompass a diverse and highly endemic fish fauna that might be sensitive to the introduction of non-native species, an ongoing process that started two centuries ago, but has to date...

The Southern Darwin’s frog Rhinoderma darwinii is a charismatic, mouth-brooding amphibian endemic to temperate forests of South America with a Vulnerable conservation status according to the IUCN Red List. We developed microsatellite markers from next generation sequence data that will aid genetic monitoring during and after re-introduction efforts...

Biological invasions create complex eco-logical and societal issues worldwide. Most of the knowledge about invasions comes only from success-ful invaders, but less is known about which processes determine the differential success of invasions. In this review, we develop a framework to identify the main dimensions driving the success and failure of...

We deep-sequenced the transcriptome of Chinook salmon (Oncorhynchus tshawytscha) that yielded 2.5 million high-quality reads (combined for four fish) with an average length of 378 bp. De novo assembly resulted in 44,264 contigs with an average length of 567 bp and an average depth of 29 reads. Nearly half (42%) of the contigs were annotated through...

List of SNP loci used in genotyping.

Sequence and primer data associated with each novel SNP developed during this study.

Numerous empirical studies have reported lack of migration-drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in Northern latitudes s...

We estimated local and metapopulation effective sizes ( and meta-) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that might be inversely related to within-species population divergence as reported in an earli...

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and contemporary collections of Alaskan sockeye salmon (Oncorhynchus nerka) to evaluate the stability of allele frequencies over 25-42 years (4.9-8.4 generations). First, our results show that temporal changes were dramatically (between 40- and 250-...

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and con-temporary collections of Alaskan sockeye salmon (Oncorhynchus nerka) to evaluate the stability of allele frequencies over 25–42 years (4.9–8.4 generations). First, our results show that temporal changes were dramatically (between 40-and 250-...

We used pyrosequencing to characterize the transcriptome of four male Chinook salmon (Oncorhynchus tshawytscha) collected from four populations throughout Puget Sound (George Adams, Soos Creek, North Fork Stillaguamish, and Marblemount). Our goal was to use the transcriptome as a source of novel and informative single nucleotide polymorphisms (SNPs...

Hierarchical analysis of molecular variance (AMOVA) between sockeye salmon populations

Pairwise FST values and tests of differentiation between Kvichak River sockeye salmon populations

Habitat and life-history attributes of three spawning ecotypes of sockeye salmon

Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka) populations from th...

Landscape genetics holds promise for the forecasting of spatial patterns of genetic diversity based on key environmental features. Yet, the degree to which inferences based on single species can be extended to whole communities is not fully understood. We used a pristine and spatially structured community of three landlocked salmonids (Salvelinus f...

A suite of 10 microsatellite loci was used to examine genetic divergence between two sympatric morphs of Arctic charr Salvelinus alpinus (‘dark’ and ‘pale’) inhabiting Gander Lake, Newfoundland. Results can be summarized as follows: (1) the morphs are strongly reproductively isolated – gene flow–migration estimates were consistently low in long and...

We combine temporal estimates of variance effective population size (Ne) and spatial genetic structure analyses from darkblotched rockfish (Sebastes crameri) to analyze the theoretical relationship between FST and population assignment (PA) of individuals to their site of origin under different migration scenarios. Although FST is the most common p...

The black rockfish (Sebastes melanops) is a long-lived (≤50 years) viviparous species with an extended pelagic larval period (3-5 months) and a broad continental distribution. Prolonged larval periods have been assumed to lead to widespread dispersal resulting in minimal population structure. We tested this assumption by comparing otolith microchem...

By pooling or removing samples of small size, we investigated how results from microsatellite analyses of spatial genetic structure in darkblotched rockfish (Sebastes crameri) were affected. Genotypes from six and seven microsatellite loci from 1206 specimens collected offshore from Washington to California were employed in the analyses. Sample siz...

The isolation and characterization of nine polymorphic microsatellite loci (eight tetranucleotide and one dinucleotide) from the canary rockfish Sebastes pinniger are described. Polymorphism at these loci revealed from six to 28 alleles, with expected heterozygosities ranging between 0.42 and 0.88, enabling high-resolution genetic population struct...

Management plans and stock assessment of exploited marine invertebrates should consider information on the genetic population structure of the species. In this context, the genetic diversity within and between populations of the commercially exploited hairy edible crab Cancer setosus was investigated using allozyme and AFLP (Amplified Fragment Leng...