Biology subjects

Canales-Aguirre, C. B.

Publications and source records attributed to Canales-Aguirre, C. B..

4 recordsLinked to original sources

bioRxiv2025

Near telomere-to-telomere genome assembly of the Chilean jack mackerel Trachurus murphyi

The Chilean jack mackerel (Trachurus murphyi) is an economically important pelagic fish widely distributed across the South Pacific Ocean. Due to intense fishing pressure and the lack of high-quality genomic resources, the development of sustainable fisheries management strategies has been hindered. Here, we present a near telomere-to-telomere genome assembly of T. murphyi using PacBio and Hi-C sequencing data. The assembled genome spans 818.31 Mb, with a contig N50 length of 24.89 Mb and a scaffold N50 length of 34.34 Mb. The assembly is anchored on 24 pseudo-chromosomes, covering 95.80% of the genome. BUSCO analysis indicates a high level of completeness at 99.0%, and telomeres and centromeres were identified on pseudo-chromosomes. Repetitive sequences account for 24.24% of the total genome, and 47,734 protein-coding genes were annotated, 90.98% of them with assigned function. Comparative genomics analyses reveal strong synteny with its congeneric Trachurus species. This high-quality genome assembly serves as a valuable resource for studying the genetic diversity and population structure of the Chilean jack mackerel and provides a solid foundation for future management and conservation efforts.

genomics↗

bioRxiv2024

Genomic signals of local adaptation in Eleginops maclovinus from Northern Chilean Patagonia

Understanding the evolutionary mechanisms that shape the adaptive divergence across spatially heterogeneous environments is a challenging task for evolutionary ecologists. The Chilean marine Patagonia is a complex ecosystem with diverse geomorphology and physical-chemical oceanographic conditions. There is limited research evaluating the interactions between selective forces and environmental conditions in this area. This study focuses on identifying the genomic signals of local adaptation of the endemic marine fish, Eleginops maclovinus from Chilean North Patagonia. To achieve this goal, we used an environmental marine database (temperature, salinity, oxygen, phosphate nitrate and silicate concentration) with collected from 1995 to 2018 and 11,961 SNPs obtained from 246 individuals from 10 sampling locations across this area. We identified putative adaptive loci using ten bioinformatic software tools, where five were based on population genetic differentiation (PGD) and five based on the genotype-environment association (GEA). We identified 392 adaptative loci using PGD and 2,164 associated with at least one of the six environmental variables analyzed using GEA. A total of 131 loci were shared between the PGD and GEA approaches, of which 37 were associated with genes involved in the growth, metabolism and homeostasis. Then, we evaluated the variation of adaptive loci with environmental variables using polygenic scores and found significant correlations with temperature, salinity, and oxygen, indicating polygenic selection along environmental gradients. This study highlights how polygenic selection drives local adaptation in Eleginops maclovinus and underscores the value of integrating genomic and environmental data for conservation in the Patagonian ecosystem.

evolutionary biology↗

bioRxiv2024

Temporal and spatial population genetic variation in Chilean jack mackerel, Trachurus murphyi

The Trachurus murphyi have been studied for population genetic structure for decades, identifying only one large population across the South Pacific Ocean. Although all these studies have extensively examined the spatial genetic pattern, there remains a gap in understanding the potential role of temporality. Our study aims to elucidate temporal and spatial genetic patterns in T. murphyi populations in the South Pacific Ocean, examining genetic composition across seasons, including feeding and spawning seasons, where the latter was not previously investigated. Using 10 microsatellite loci, our study confirms a consistent and stable population genetic pattern in T. murphyi across its geographic distribution, observed over multiple years and seasons. Furthermore, we identify potential genetic markers for monitoring variability in the species.

genetics↗

bioRxiv2020

Shrinking of fish under warmer temperatures decrease dispersal abilities and speciation rates

There is an ongoing debate as to whether fish body size will decrease with global warming and how body size changes may impact dispersal abilities and speciation rates. Although theory predicts that, when fish face warmer temperatures, they grow to smaller adult sizes, see a reduction in their ability to move, and increase their probability of speciation, evaluations of such predictions are hampered owing to the lack of empirical data spanning both wide temporal and geographical scales. Here, using phylogenetic methods, temperature, and 21,895 occurrences for 158 worldwide-distributed species of fish, we show that smaller fish have occurred in warmer waters for over 150 million years and across marine and freshwater realms. Smaller fish have historically moved the shortest distances and at low speeds. In addition, small fish display the lowest probability of giving rise to new species. Further, we found that species of fish that displayed high speeds of geographical movement and rates of size evolution experienced higher rates of temperature change in their lineage. Taking these results together, global warming predicts a future where smaller fish that have reduced ability to move over aquatic systems will be more prevalent, in turn, this will result in fewer species contributing global biodiversity.

evolutionary biology↗