Dynamics of Two Anadromous Species in a Dam Intersected River: Analysis of Two 100-Year Datasets

Long-term time-series datasets are key for assessing the population dynamics of fish species with economic interest. This study examines two 100-year datasets for sea lamprey Petromyzon marinus and allis shad Alosa alosa from the Minho River. This basin on the Iberian Peninsula is home to one of the largest populations at the southern distribution limit of these critically endangered anadromous fish species. Besides assessing the importance of the environmental drivers of fish capture data (temperature, salinity, upwelling, precipitation, and climatic oscillation), this study also assesses how dam construction affected these populations using intervention analysis—A statistical tool to detect significant breakpoints in time series data. Results showed contrasting trends between sea lamprey and allis shad, with the number of captured fish from the first progressively improving from 1914 to 2017, and the latter recording a significant decline over time. Although no significant correlations were detected between fishing data and environmental variables, some of the identified breakpoints in the time series data matched the dates when the major dams in Minho River were built. Other historical activities associated with mining might explain the notable changes detected in the trends, while issues associated with illegal, unreported, and unregulated capture data are also discussed.

Comprehensive phylogeny of Konosirus punctatus (Clupeiformes: Clupeidae) based on transcriptomic data

Konosirus punctatus is an important species for the structure of marine ecosystems. Meanwhile, it is a native species in the northwest Pacific Ocean and supports important commercial fishery. In this study, we generated the whole transcriptome of K. punctatus from combined tissues (muscle, liver, gill, heart, kidney, swim bladder and sexual gland) using Illumina RNA-seq technology and a total of 46,087,110 clean reads were obtained, corresponding to 6,531,521,430 nucleotides. Meanwhile, 10,000 clean reads were random selected and compared with NT database to examine the possible contamination. Results showed that 6,754 clean reads were distributed among some species closely related with K. punctatus, indicating no-pollution. De novo assembly was performed and all clean reads were assembled to produce 71,610 longest unigenes with an N50 of 906 bp. Among all the unigenes, 43,974 unigenes were annotated in at least one database and 3,172 unigenes were annotated in all databases. All unigenes were further analyzed to predict the gene structure and we have obtained a total of 54,864 coding sequences (CDS) and 17,326 simple sequence repeats (SSRs). Saturation analyses were applied to evaluate the accuracy of gene expression and we hypothesized that the detection of gene expression might be effective. Finally, single-copy orthologous genes were applied to construct the phylogenetic relationship of K. punctatus. Results showed that K. punctatus diverged from the common ancestor with Alosa alosa, A. pseudoharengus and Sardina pilchardus around 61.16-92.52 MYA. The present study will provide a foundational molecular information for the biological research of K. punctatus.

A new approach combining forensic thresholds and a multiple-tubes approach to unravel false microsatellite profiles from cross-contaminated sample material

Contamination and degradation are known challenges for reliable genotyping, since they can cause, among other problems, false microsatellite profiles. In this study we described a method to decrease the proportion of false microsatellite profiles from fish scale samples of endangered allis shads (Alosa alosa) from a reintroduction program, where cross-contamination with DNA from other individuals and potentially degradation of samples occurred. To maximize the portion of reliably measurable results, we modified and combined two known approaches—thresholds used in forensic DNA analyses and a multiple-tubes approach. This combined approach increased reliable microsatellite profiles compared with single approaches. The forensic thresholds and the multiple-tubes approach increased the measurable results from 55 to 67% and 75%, respectively, whereas the combined approach accomplished an increase to 90%. This illustrates the potential of the combined approach for other studies with comparable problems or sample material.

1980s population-specific compositions of two related anadromous shad species during the oceanic phase determined by microchemistry of archived otoliths

The specific stock composition and dispersion of anadromous fish species aggregations in the marine environment are poorly known, while they can play a major role in the metapopulation dynamics. Otolith microchemistry has proven to be a powerful tool to address natal origins of anadromous fish. We used archived otolith microchemistry to investigate the population-specific composition of subadult European shads (Alosa alosa and Alosa fallax) in the ocean during the 1980s. The allocation of natal origin was addressed relying on contemporary water and juveniles’ signatures within a Bayesian model. A great discrimination of natal origin was obtained at the Biscay Gulf scale. However, the discrimination of 1980s natal origin for the southern rivers with similar geology based on 2013 water and juveniles’ baselines was doubtful. Our results showed that the most abundant southern populations were dominant, suggesting that population-specific composition was related to population relative abundance. The dispersion in the marine environment was plastic; alternatively, shads were found large distances away from their natal rivers, while others remained in the vicinity of their natal river plume.