Spatio-temporal patterns of genetic variations in populations of yellowtail kingfish Seriola lalandi from the south-eastern Pacific Ocean and potential implications for its fishery management

Otolith Weight as an Estimator of the Age of Seriola lalandi Valenciennes, 1833 (Carangidae), in the Southeastern Pacific

Simple Summary

The healthy management of fishery resources requires the evaluation of a series of population attributes, such as mortality, fecundity, spawning biomass, recruitment and the age at which fish reach sexual maturity. All these attributes depend on the age of fish. Then, the adequate administration and management of these resources require estimators of fish age. Age is estimated by ring counts in the otoliths, which are hard and calcified structures responsible for the balance of fish; however, this is an expensive and time-consuming methodology. An alternative is the use of otolith weight due to its expected relationship with fish age. Yellowtail king fish is a valuable resource, which arrives at the Chilean northern coast in the summer (southern hemisphere). Many aspects of the biology of this fish, such as age and growth, remain unknown. In this study, we estimated the age and growth using otolith weight, which was measured from fish with a known age, and we calculated parameters explaining growth using four different models. The best model was the seasonalized von Bertalanffy growth function, which takes into account that fish do not grow at the same rate year round.

Abstract

The age and growth of fish populations is a critical issue for stock assessment, population dynamics and fishery management. Spawner biomass, mortality, growth, recruitment and age at maturity can be misconstrued if the age estimator is inaccurate. Age can be estimated by annuli count, but this requires expertise and is expensive. Otolith weight (OW) is a good indicator of how long a fish has lived, because OW increases during an individual’s life. Seriola lalandi is a migratory fish and is an important resource for local fishermen in northern Chile. Aspects of its biology, i.e., age and growth, remain unknown, at least for the population annually arriving in northern Chile. Fish of a known age (n = 105; from 5.5 to 25.7 cm in FL) from yellowtail aquaculture facilities at Universidad de Antofagasta allowed us to estimate the growth rate of OW, and fish obtained from local fishermen (n = 71; from 37.9 to 109 cm in FL) allowed us to estimate the age and growth of S. lalandi from the analysis of OW, without the need for calibration. The following four models were fitted with the known ages and fork lengths: the von Bertalanffy growth function, the Gompertz and logistic models and the seasonalized von Bertalanffy growth function. The latter model showed the best adjustment (according to the Akaike information criterion) with the following parameters: L_∞, 98.58 cm.; K, 0.59; t₀, 0.07; t_s, 0.84; and C, 0.97.

First Report of Blood Fluke Pathogens with Potential Risk for Emerging Yellowtail Kingfish (Seriola lalandi) Aquaculture on the Chilean Coast, with Descriptions of Two New Species of Paradeontacylix (Aporocotylidae)

Blood flukes are digeneans that infect wild and farmed fish that can cause a severe and potentially lethal disease in farmed fish. These parasites are undetectable in the larval stage based on macroscopic observations in the definitive host with the infection becoming evident when eggs accumulate in the branchial vessels. There are nine known species of the genus Paradeontacylix and seven exclusively parasitize Seriola spp. from several geographical areas. Seriola lalandi aquaculture farms are emerging at various localities in northern Chile. Here, we report, for the first time, two blood fluke species parasitizing S. lalandi in the Southeastern Pacific (Chile). In the laboratory, the gills and heart of fish were removed. The retained blood flukes were separated according to the infection site, fixed in 70% or 95% ethanol for taxonomic and molecular analysis, respectively. Morphometrical differences among the fluke species were evaluated with a principal component analysis (PCA) using proportional body measurements. Phylogenetic trees were constructed based on 28S rDNA, cox1 mDNA using Bayesian inference (BI), and maximum likelihood (ML). Based on morphology, morphometry, and molecular analyses, two new species are proposed: P. humboldti n. sp. from the gills and P. olivai n. sp. from the heart of S. lalandi. Both were clearly distinguished from other species of Paradeontacylix by a combination of morphologic features (posterior tegumental spines, testes arrangement, body size). The genetic distance (based on cox1) among species was >10%. P. humboldti n. sp. and P. olivai n. sp. are sister species (with a common ancestor) independent of P. godfreyi from S. lalandi in Australia. The newly identified parasites may pose a risk to farmed S. lalandi as aporocotylids have been the cause of diseases in farmed fish from other geographical areas. In addition, some cages of S. lalandi are currently maintained in an open circulating system, which could favor the transmission of these parasites (if involved hosts are present in the environment).

Genetic diversity and structure of circumtropical almaco jack, Seriola rivoliana: tool for conservation and management

The almaco jack, Seriola rivoliana, is a circumtropical pelagic fish of importance both in commercial fisheries and in aquaculture. To understand levels of genetic diversity within and among populations in the wild, population genetic structure and the relative magnitude of migration were assessed using mtDNA sequence data and single nucleotide polymorphisms (SNPs) from individuals sampled from locations in the Pacific and Atlantic Oceans. A total of 25 variable sites of cytochrome c oxidase subunit 1 and 3678 neutral SNPs were recovered. Three genetic groups were identified, with both marker types distributed in different oceanic regions: Pacific-1 in central Pacific, Pacific-2 in eastern Pacific and Atlantic in western Atlantic. Nonetheless, the analysis of SNP identified a fourth population in the Pacific coast of Baja California Sur, Mexico (Pacific-3), whereas that of mtDNA did not. This mito-nuclear discordance is likely explained by a recently diverged Pacific-3 population. In addition, two mtDNA haplogroups were found within the western Atlantic, likely indicating that the species came into the Atlantic from the Indian Ocean with historical gene flow from the eastern Pacific. Relative gene flow among ocean basins was low with _r m < 0.2, whereas in the eastern Pacific it was asymmetric and higher from south to north (_r m > 0.79). The results reflect the importance of assessing genetic structure and gene flow of natural populations for the purposes of sustainable management.

Time matters: genetic composition and evaluation of effective population size in temperate coastal fish species

Background

Extensive knowledge on the genetic characterization of marine organisms has been assembled, mainly concerning the spatial distribution and structuring of populations. Temporal monitoring assesses not only the stability in genetic composition but also its trajectory over time, providing critical information for the accurate forecast of changes in genetic diversity of marine populations, particularly important for both fisheries and endangered species management. We assessed fluctuations in genetic composition among different sampling periods in the western Portuguese shore in three fish species.

Methods

White seabream Diplodus sargus, sand smelt Atherina presbyter and shanny Lipophrys pholis were chosen, because of their genetic patterns in distinct ecological environments, insight into historical and contemporary factors influencing population effective size (N_e), and degree of commercial exploitation. Samples were obtained near Lisbon between 2003 and 2014 and screened for genetic variation with mitochondrial and nuclear markers. Analyses included genealogies, genetic diversities, temporal structures and contemporary N_e.

Results

For mtDNA no temporal structure was detected, while for nDNA significant differences were recorded between some sampling periods for the shanny and the sand smelt. Haplotype networks revealed deep genealogies, with various levels of diversification. The shanny revealed a smaller N_e/generation when compared to the other species, which, in turn, revealed no evidence of genetic drift for most study periods. These results highlight the fact that temporal variations in genetic pool composition should be considered when evaluating the population structure of fish species with long distance dispersal, which are more vulnerable to recruitment fluctuations.

First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi

The genetic resources available for the commercially important fish species Yellowtail kingfish (YTK) (Seriola lalandi) are relative sparse. To overcome this, we aimed (1) to develop a linkage map for this species, and (2) to identify markers/variants associated with economically important traits in kingfish (with an emphasis on body weight). Genetic and genomic analyses were conducted using 13,898 single nucleotide polymorphisms (SNPs) generated from a new high-throughput genotyping by sequencing platform, Diversity Arrays Technology (DArTseq^TM) in a pedigreed population comprising 752 animals. The linkage analysis enabled to map about 4,000 markers to 24 linkage groups (LGs), with an average density of 3.4 SNPs per cM. The linkage map was integrated into a genome-wide association study (GWAS) and identified six variants/SNPs associated with body weight (P < 5e^-8) when a multi-locus mixed model was used. Two out of the six significant markers were mapped to LGs 17 and 23, and collectively they explained 5.8% of the total genetic variance. It is concluded that the newly developed linkage map and the significantly associated markers with body weight provide fundamental information to characterize genetic architecture of growth-related traits in this population of YTK S. lalandi.

Genomic DNA variation confirmed Seriola lalandi comprises three different populations in the Pacific, but with recent divergence

Captive breeding programs and aquaculture production have commenced worldwide for the globally distributed yellowtail kingfish (Seriola lalandi), and captive bred fingerlings are being shipped from the Southern Hemisphere to be farmed in the Northern Hemisphere. It was recently proposed that Pacific S. lalandi comprise at least three distinct species that diverged more than 2 million years ago. Here, we tested the hypothesis of different “species” in the Pacific using novel genomic data (namely single nucleotide polymorphisms and diversity array technology markers), as well as mtDNA and DNA microsatellite variation. These new data support the hypothesis of population subdivision between the Northeast Pacific, Northwest Pacific and South Pacific, and genetic divergence indicates restriction to the gene flow between hemispheres. However, our estimates of maximum mtDNA and nuclear DNA divergences of 2.43% and 0.67%, respectively, were within the ranges more commonly observed for populations within species than species within genera. Accordingly our data support the more traditional view that S. lalandi in the Pacific comprises three distinct populations rather than the subdivisions into several species.