Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot.

Marine biodiversity can be surveyed using underwater visual censuses and recently with eDNA metabarcoding. Although a promising tool, eDNA studies have shown contrasting results related to its detection scale and the number of species identified compared to other survey methods. Also, its accuracy relies on complete reference databases used for taxonomic assignment and, as other survey methods, species detection may show false-negative and false-positive errors. Here, we compared results from underwater visual censuses and simultaneous eDNA metabarcoding fish surveys in terms of observed species and community composition. We also assess the effect of a custom reference database in the taxonomic assignment, and evaluate occupancy, capture and detection probabilities, as well as error rates of eDNA survey data. We amplified a 12S rRNA fish barcode from 24 sampling sites in the gulf of California. More species were detected with eDNA metabarcoding than with UVC. Because each survey method largely detected different sets of species, the combined approach doubled the number of species registered. Both survey methods recovered a known biodiversity gradient and a biogeographic break, but eDNA captured diversity over a broader geographic and bathymetric scale. Furthermore, the use of a modest-sized custom reference database significantly increased taxonomic assignment. In a subset of species, occupancy models revealed eDNA surveys provided similar or higher detection probabilities compared to UVC. The occupancy value of each species had a large influence on eDNA detectability, and in the false positive and negative error. Overall, these results highlight the potential of eDNA metabarcoding in complementing other established ecological methods for studies of marine fishes.

Phylogeography and Ecological Niche Modeling of the Desert Iguana (Dipsosaurus dorsalis, Baird & Girard 1852) in the Baja California Peninsula.

Understanding the factors that explain the patterns of genetic structure or phylogeographic breaks at an intraspecific level is key to inferring the mechanisms of population differentiation in its early stages. These topics have been well studied in the Baja California region, with vicariance and the dispersal ability of individuals being the prevailing hypothesis for phylogeographic breaks. In this study, we evaluated the phylogeographic patterns in the desert iguana (Dipsosaurus dorsalis), a species with a recent history in the region and spatial variation in life history traits. We analyzed a total of 307 individuals collected throughout 19 localities across the Baja California Peninsula with 15 microsatellite DNA markers. Our data reveal the existence of 3 geographically discrete genetic populations with moderate gene flow and an isolation-by-distance pattern presumably produced by the occurrence of a refugium in the Cape region during the Pleistocene Last Glacial Maximum. Bayesian methods and ecological niche modeling were used to assess the relationship between population genetic structure and present and past climatic preferences of the desert iguana. We found that the present climatic heterogeneity of the Baja California Peninsula has a marked influence on the population genetic structure of the species, suggesting that there are alternative explanations besides vicariance. The information obtained in this study provides data allowing a better understanding of how historical population processes in the Baja California Peninsula can be understood from an ecological perspective.

Isolation and characterization of 14 tetranucleotide microsatellite loci for the cannonball jellyfish (Stomolophus sp.) by next generation sequencing.

The Cannonball jellyfish (Stomolophus sp.) is a species of jellyfish with high relevance in artisanal fishing. Studies of their populations do not extend beyond the morphological descriptions knowing that presents a great morphological variability. However, there are no genetic studies to determine the number of independent populations, so microsatellite markers become a suitable option. Since there are no species-specific microsatellite loci, in this paper, 14 new microsatellite loci are characterized. Microsatellite loci were isolated de novo through next generation sequencing, by two runs on Illumina MiSeq. A total of 506,771,269 base pair were obtained, from which 142,616 were microsatellite loci, and 1546 of them could design primers. We tested 14 primer pairs on 32 individuals from Bahía de La Paz, Gulf of California. We observed low genetic variation among loci (mean number of alleles per locus = 4.33, mean observed heterozygosity 0.381, mean expected heterozygosity 0.501). These loci are the first ones described for the species and will be helpful to carry out genetic diversity and population genetics studies.

Coping with potential bi-parental inbreeding: limited pollen and seed dispersal and large genets in the dioecious marine angiosperm Thalassia testudinum.

The high prevalence of dioecy in marine angiosperms or seagrasses (>50% of all species) is thought to enforce cross-fertilization. However, seagrasses are clonal plants, and they may still be subject to sibling-mating or bi-parental inbreeding if the genetic neighborhood is smaller than the size of the genets. We tested this by determining the genetic neighborhoods of the dioecious seagrass Thalassia testudinum at two sites (Back-Reef and Mid-Lagoon) in Puerto Morelos Reef Lagoon, Mexico, by measuring dispersal of pollen and seeds in situ, and by fine-scale spatial autocorrelation analysis with eight polymorphic microsatellite DNA markers. Prevalence of inbreeding was verified by estimating pairwise kinship coefficients; and by analysing the genotypes of seedlings grown from seeds in mesocosms. Average dispersal of pollen was 0.3-1.6 m (max. 4.8 m) and of seeds was 0.3-0.4 m (max. 1.8 m), resulting in a neighborhood area of 7.4 m2 (range 3.4-11.4 m2) at Back-Reef and 1.9 (range 1.87-1.92 m2) at Mid-Lagoon. Neighborhood area (Na) derived from spatial autocorrelation was 0.1-20.5 m2 at Back-Reef and 0.1-16.9 m2 at Mid-Lagoon. Maximal extensions of the genets, in 19 × 30 m plots, were 19.2 m (median 7.5 m) and 10.8 m (median 4.8 m) at Back-Reef and Mid-Lagoon. There was no indication of deficit or excess of heterozygotes nor were coefficients of inbreeding (FIS) significant. The seedlings did not show statistically significant deficit of heterozygotes (except for 1 locus at Back-Reef). Contrary to our expectations, we did not find evidence of bi-parental inbreeding in this dioecious seagrass with large genets but small genetic neighborhoods. Proposed mechanisms to avoid bi-parental inbreeding are possible selection against homozygotes during fecundation or ovule development. Additionally, the genets grew highly dispersed (aggregation index Ac was 0.09 and 0.10 for Back-Reef and Mid-Lagoon, respectively); such highly dispersed guerrilla-like clonal growth form likely increases the probability of crossing between different potentially unrelated genets.