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Abstract The deep sea (>200 m) is home to a surprisingly rich biota, which in some cases compares to that found in shallow areas. Scleractinian corals are an example of this – they are key species in both shallow and deep ecosystems. However, what evolutionary processes resulted in current depth distribution of the marine fauna is a long-standing question. Various conflicting hypotheses have been proposed, but few formal tests have been conducted. Here, we use global spatial distribution data to test the bathymetric origin and colonization trends across the depth gradient in scleractinian corals. Using a phylogenetic approach, we infer the origin and historical trends in directionality and speed of colonization during the diversification in depth. We also examine how the emergence of photo-symbiosis and coloniality, scleractinian corals’ most conspicuous phenotypic innovations, have influenced this process. Our results strongly support an offshore-onshore pattern of evolution and varying dispersion capacities along depth associated with trait-defined lineages. These results highlight the relevance of the evolutionary processes occurring at different depths to explain the origin of extant marine biodiversity and the consequences of altering these processes by human impact, highlighting the need to include this overlooked evolutionary history in conservation plans.

Abstract Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better‐studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better‐resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.

Abstract Background Human population growth since the mid-1900s has been accompanied by an unsustainable use of natural resources and a corresponding impact on terrestrial and marine biota. In response, most states have established protected areas as tools to decrease biodiversity loss, being Chile one of the signatories of international conservation agreements such as the Convention on Biological Diversity (CBD) and the 2010 Aichi Targets. This study reviews the Chilean protected areas that have been created to date, with an emphasis on the existence and effectiveness of management plans for all terrestrial and marine protected areas. Effectiveness was individually evaluated using two filters: 1) the age of the management plan and 2) the first four steps of the Protected Areas Management Effectiveness (PAME) methodology recommended by the IUCN. Results We show that 84 out of a total of 145 protected areas (PAs), and only five out of a total of 20 marine protected areas (MPAs), have management plans. Only 12% (N = 16) of PAs are effectively managed; while in the marine realm, no MPA has an effective plan. Conclusions Our results show the lack of both the effectiveness of and updates to the management plans for the vast majority of the national territory and raise the following question: is it sustainable to continue adding protected areas to the national system even though it is clear that the existing support is insufficient to meet the minimum requirements for full implementation?