Species detected from eDNA analysis with ObiTools
In the Willemstad area, eDNA analysis detected a total of 33 taxa assigned to species level, 47 assigned to the genus level and 44 to the family level (Table S1). Among these, 7 species, 8 genera and 7 families were unique to this area. Those species, genera and families included typical demersal species of shallow coastal waters such as the Albulidae, Gerreidae, Elopidae associated to sand soft bottoms and Achiridae, Eleotridae associated with mud soft bottoms and brackish waters (Table S1). In Valentijnsbaai area, we detected a total of 36 taxa assigned to species level, 50 assigned to the genus level and 41 to the family level (Table S1). Among these, 11 species, 8 genera and 4 families occurred exclusively in this area. Among those exclusive species, genera and families, two families were pelagic, Istiophoridae and Myliobatidae. The two remaining families were Moringuidae and Aetobatidae, comprised of demersal species associated with coastal ecosystems such as reefs and estuaries exclusively present in the area – including Moringua edwardsi and Aetobatus narinari , respectively (Table S1). In both areas, we detected the presence of species from the families Gobiidae and Apogonidae, which include the majority of crypto benthic species, an important component of reef systems (Brandl et al. 2018). One filter did not yield sufficient DNA for reliable analyses and we removed it. The eDNA analyses are presented for the 19 remaining filters.
Underwater visual census (UVC) at the stations in front of Willemstad recorded a total of 30 families, 56 genera and 99 species. Among the species in common with both methods, reef associated species such as theHalichoeres spp or Chromis multilineata were recorded by UVC and eDNA, while typical crypto benthic species such asPhaeoptyx conklini, P. pigmentaria and Priolepis hipoliti ; and pelagic species such as Carcharhinus longimanus orAcanthocybium solandri or coastal species such as Erotelis smaragdus and Mugil rubrioculus were only detected by eDNA. The detection of those species by eDNA is supported by the known occurrence of those species in Willemstad based on species range maps of the species in the Caribbean region (Supplementary Table 1). At the genus level, eleven detected genera were common in both methods and 16 were detected exclusively with eDNA. At the family level, nine detected families were common in both methods and nine families were detected exclusively with eDNA. Some reef families such Gobiidae, Labridae and Pomacentridae were recorded by both UVC and eDNA, while typical pelagic such as Clupeidae, Myctophidae and Neoscopelidae and demersal families such as Eleotridae and Mugilidae were detected by eDNA. In Valentijnsbaai area, UVC recorded a total of 33 families, 59 genera and 97 species. Reef associated species such as the Halichoeres sppor Bodianus rufus were recorded by both UVC and eDNA, while typical crypto benthic species such as Elacatinus horsti ,Lophogobius cyprinoides and Oxyurichthys stigmalophius ; or classic reef top predators such as Carcharinus perezii , were only detected by eDNA. At the genus level, nine detected genera were common in both methods and 19 were detected exclusively with eDNA. At the family level, nine detected families were common in both methods and nine families were detected exclusively with eDNA. Some reef families such Apogonidae, Gobiidae and Labridae were recorded by both UVC and eDNA, while typical pelagic families such as Carcharhinidae, Clupeidae and Myctophidae were detected by eDNA.