DNA-metabarcoding supports trophic flexibility and reveals new prey species for the Galapagos sea lion.

Tropical ecosystems are challenging for pinnipeds due to fluctuating food availability. According to previous research, the Galapagos sea lion (GSL, Zalophus wollebaeki) adopts trophic flexibility to face such conditions. However, this hypothesis comes from studies using traditional methods (hard-parts analysis of scat and isotopic analysis from tissue). We studied the diet of five rookeries in the southeastern Galapagos bioregion (which harbors the highest GSL density), via DNA-metabarcoding of scat samples. The DNA-metabarcoding approach may identify consumed prey with a higher taxonomic resolution than isotopic analysis, while not depending on hard-parts remaining through digestion. Our study included five different rookeries to look for evidence of trophic flexibility at the bioregional level. We detected 98 prey OTUs (124 scats), mostly assigned to bony-fish taxa; we identified novel prey items, including a shark, rays, and several deep-sea fish. Our data supported the trophic flexibility of GSL throughout the studied bioregion since different individuals from the same rookery consumed prey coming from different habitats and trophic levels. Significant diet differentiations were found among rookeries, particularly between Punta Pitt and Santa Fe. Punta Pitt rookery, with a more pronounced bathymetry and lower productivity, was distinguished by a high trophic level and consumption of a high proportion of deep-sea prey; meanwhile, Santa Fe, located in more productive, shallow waters over the shelf, consumed a high proportion of epipelagic planktivorous fish. Geographic location and heterogeneous bathymetry of El Malecon, Española, and Floreana rookeries would allow the animals therein to access both, epipelagic prey over the shelf, and deep-sea prey out of the shelf; this would lead to a higher prey richness and diet variability there. These findings provide evidence of GSL adopting a trophic flexibility to tune their diets to different ecological contexts. This strategy would be crucial for this endangered species to overcome the challenges faced in a habitat with fluctuating foraging conditions.

Time-calibrated phylogeny and full mitogenome sequence of the Galapagos sea lion (Zalophus wollebaeki) from scat DNA.

Background: The Galapagos sea lion, Zalophus wollebaeki, is an endemic and endangered otariid, which is considered as a sentinel species of ecosystem dynamics in the Galapagos archipelago. Mitochondrial DNA is an important tool in phylogenetic and population genetic inference. In this work we use Illumina sequencing to complement the mitogenomic resources for Zalophus genus-the other two species employed Sanger sequencing-by a complete mitochondrial genome and a molecular clock of this species, which is not present in any case. Materials and Methods: We used DNA obtained from a fresh scat sample of a Galapagos sea lion and shotgun-sequenced it on the Illumina NextSeq platform. The obtained raw reads were processed using the GetOrganelle software to filter the mitochondrial Zalophus DNA reads (∼16% survive the filtration), assemble them, and set up a molecular clock. Results: From the obtained 3,511,116 raw reads, we were able to assemble a full mitogenome of a length of 16,676 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA), and two ribosomal RNAs (rRNA). A time-calibrated phylogeny confirmed the phylogenetic position of Z. wollebaeki in a clade with Z. californianus, and Z. japonicus, and sister to Z. californianus; as well as establishing the divergence time for Z. wollebaeki 0.65 million years ago. Our study illustrates the possibility of seamlessly sequencing full mitochondrial genomes from fresh scat samples of marine mammals.

Detection and quantification of microplastic pollution in the endangered Galapagos sea lion.

Marine debris pollution poses a significant global threat to biodiversity, with plastics being the primary debris type found in oceans due to their low-cost production and high demand worldwide. Microplastics (MPs, <5 mm in size) are highly bioavailable to a wide range of marine taxa, including marine mammals, through direct and indirect ingestion routes (i.e., trophic transfer). Recently, MP pollution has been detected on the Galapagos Marine Reserve, so in this study we developed a baseline framework for MP pollution in the Galapagos sea lion (GSL, Zalophus wollebaeki) through scat-based analysis. We collected 180 GSL scat samples from the southeast region following strict quality assurance/quality control protocols to detect, quantify and characterize physical-chemical properties of MPs through visual observations and µFT-IR spectroscopy. We recovered 81 MPs of varying sizes and colors in 37 % of samples (n = 66/180), consisting mostly of fibers (69 %, x¯ = 0.31 ± 0.57 particles scat-1). The number of particles per gram of sample wet weight ranged from 0.02 to 0.22 (x¯ = 0.04 ± 0.05 particles scat wet g-1). El Malecón and Punta Pitt rookeries at San Cristobal Island had the highest number of MPs (x¯ = 0.67 ± 0.51 and 0.43 ± 0.41 particles scat-1, respectively), and blue-colored particles were the most common in all samples. We identified eleven polymers in 46 particles, consisting mostly of polypropylene-polyethylene copolymer, polypropylene, cellulose, polyethylene, and polyvinyl chloride. The textile, fishing, and packaging industries are likely significant sources of microfibers into this insular ecosystem. Our results suggest that the GSL is exposed to MPs due to anthropogenic contamination that is subsequently transferred through trophic processes. These findings provide an important baseline framework and insights for future research on MP pollution in the region, as well as for management actions that will contribute to the long-term conservation of the GSL.