Environmental DNA (eDNA) metabarcoding is a new approach for assessing marine biodiversity that may overcome challenges of traditional monitoring and complement both existing surveys and biodiversity assessments. There are limited eDNA studies that evaluate vertebrate biodiversity in the marine environment or compare patterns of biodiversity with traditional methods. This study uses eDNA metabarcoding of the mitochondrial 12S rRNA genes present in seawater samples to characterize vertebrate biodiversity and distribution within National Marine Sanctuaries located in the California Current upwelling ecosystem. The epipelagic community in the study region has been monitored using traditional (mid-water trawl and marine mammal) survey methods since 1983. During 2016 and 2017, we concurrently sampled the epipelagic community using traditional survey methods and water for eDNA analysis to assess agreement among the methods. We collected replicate eDNA samples from 25 stations at depths of 10, 40, and 80 m, resulting in 131 small volume (1 L) environmental water samples to examine eDNA sequences. Across the eDNA and traditional survey methods, 80 taxa were identified. Taxa identified by eDNA partially overlapped with taxa through trawl and marine mammal surveys, but more taxa were identified by eDNA. Diversity and distribution patterns of marine vertebrates inferred from eDNA sequences reflected known spatial distribution patterns in species occurrence and community structure (e.g., cross-shelf and alongshore patterns). During both years, we identified fishery taxa Sebastes (rockfish), Merluccius (hake), Citharichthys(sanddab), and Engraulis (anchovy) across the majority of the stations using eDNA metabarcoding. The marine vertebrate assemblage identified by eDNA in 2016 was statistically different from the 2017 assemblage and more marine mammals were identified in 2017 than in 2016. Differences in assemblages identified by eDNA were coincident with different oceanographic conditions (e.g., upwelling and stratification). In 2016, weak upwelling and warmer than average conditions were measured, and vertebrate assemblages were not different among ecological regions [Point Reyes, Pescadero, and Monterey Bay]. While in 2017, average upwelling conditions returned, vertebrate assemblages differed at each region. This study illustrates that eDNA provides a new baseline for vertebrate assessments that can both augment traditional biomonitoring surveys and aid our understanding of changes in biodiversity.
Distributions of Species
Global warming is driving changes in the distribution patterns of many species, leading to a general tropicalization and meridionalization of biota. In this context, populations of some marine species are in regression while others are expanding their populations. Such is the case of benthic cnidarians belonging to the order Zoantharia and suborder Brachycnemina, whose populations are able to cause phase-shifts in coral reef ecosystems. Marine assemblages in the subtropical Canary Islands region consist of a combination of both temperate and tropical species, mainly due to the east-to-west seawater temperature gradient that naturally exists throughout the archipelago. This can reach a 2 °C difference (≈23-25 °C east to west in summer months). These biogeographical features make the archipelago a unique location to research into biota reorganisation processes. The aim of this study was to establish a baseline of the distribution and abundance data of zoantharian Brachycnemina populations in the Canary Islands. To elucidate whether these species are potential bioindicators of ocean warming processes, patterns of species distribution and their relationships with the temperature gradient across the archipelago were also evaluated. Results demonstrated that intertidal and subtidal populations of Palythoa aff. clavata and P. caribaeorum, respectively, followed distribution patterns related to the temperature ranges recorded in situ by data loggers. Extensive populations were found in the western islands where seawater temperatures are warmer than the eastern islands. Since biota reorganisation usually produces loss of ecosystem functions, it is essential to establish baseline datasets of climate change indicators and also effective monitoring programmes. These will allow early detection of phase-shifts before they lead to significant changes in ecosystem dynamics.
Most cetacean species are wide-ranging and highly mobile, creating significant challenges for researchers by limiting the scope of data that can be collected and leaving large areas un-surveyed. Aerial surveys have proven an effective way to locate and study cetacean movements but are costly and limited in spatial extent. Here we present a semi-automated pipeline for whale detection from very high-resolution (sub-meter) satellite imagery that makes use of a convolutional neural network (CNN). We trained ResNet, and DenseNet CNNs using down-scaled aerial imagery and tested each model on 31 cm-resolution imagery obtained from the WorldView-3 sensor. Satellite imagery was tiled and the trained algorithms were used to classify whether or not a tile was likely to contain a whale. Our best model correctly classified 100% of tiles with whales, and 94% of tiles containing only water. All model architectures performed well, with learning rate controlling performance more than architecture. While the resolution of commercially-available satellite imagery continues to make whale identification a challenging problem, our approach provides the means to efficiently eliminate areas without whales and, in doing so, greatly accelerates ocean surveys for large cetaceans.
The CETUS project is a cetacean monitoring program that takes advantage of cargo ships to undertake survey routes between Continental Portugal, Macaronesian archipelagos and West Africa. From 2012 to 2017, over 50 volunteers participated in the program, actively surveying more than 124.000 km, mostly beyond national jurisdictions in the high seas, for which little or no previous data existed. In total, the collection comprises 3058 georeferenced transect lines and 8913 positions, which are associated with 2833 cetacean sightings, 362 occurrences of other pelagic megafauna, 5260 estimates of marine traffic and 8887 weather observations. This dataset may provide new insights into the distribution of marine mammals in the Eastern North Atlantic and was published following the OBIS-ENV-DATA format (with the most recent biodiversity data standards at the time of writing). Consequently, it may serve as a model for similar visual line transect data collections yet to be published.
Marine habitats are nowadays strongly affected by human activities, while for many species the consequences of these impacts are still unclear. The red-throated diver (Gavia stellata) has been reported to be sensitive to ship traffic and other anthropogenic pressures and is consequently of high conservation concern. We studied red-throated divers in the German Bight (North Sea) using satellite telemetry and digital aerial surveys with the aim of assessing effects of ship traffic on the distribution and movements of this species during the non-breeding season. Data from the automatic identification system of ships (AIS) were intersected with bird data and allowed detailed spatial and temporal analyses. During the study period, ship traffic was present throughout the main distribution area of divers. Depending on impact radius, only small areas existed in which ship traffic was present on less than 20% of the days. Ship traffic was dominated by fishing vessels and cargo ships, but also wind farm-related ships were frequently recorded. Red-throated divers were more abundant in areas with no or little concurrent ship traffic. Analysis of aerial survey data revealed strong effects of ship speed on divers: in areas with vessels sailing at high speed only a slow resettlement of the area was observed after the disturbance, while in areas with vessels sailing at medium speed the resettlement was more rapid during the observed time period of 7 hours. Data from satellite-tracking of divers suggest that large relocation distances of individuals are related to disturbance by ships which often trigger birds to take flight. Effective measures to reduce disturbance could include channeled traffic in sensitive areas, as well as speed limits for ships traveling within the protected marine area.
Within the context of global climate change and overfishing of fish stocks, there is some evidence that cephalopod populations are benefiting from this changing setting. These invertebrates show enhanced phenotypic flexibility and are found from polar regions to the tropics. Yet, the global patterns of species richness in coastal cephalopods are not known. Here, among the 370 identified-species, 164 are octopuses, 96 are cuttlefishes, 54 are bobtails and bottletails, 48 are inshore squids and 8 are pygmy squids. The most diverse ocean is the Pacific (with 213 cephalopod species), followed by the Indian (146 species) and Atlantic (95 species). The least diverse are the Southern (15 species) and the Arctic (12 species) Oceans. Endemism is higher in the Southern Ocean (87%) and lower in the Arctic (25%), which reflects the younger age and the “Atlantification” of the latter. The former is associated with an old lineage of octopuses that diverged around 33 Mya. Within the 232 ecoregions considered, the highest values of octopus and cuttlefish richness are observed in the Central Kuroshio Current ecoregion (with a total of 64 species), followed by the East China Sea (59 species). This pattern suggests dispersal in the Central Indo-Pacific (CIP) associated with the highly productive Oyashio/Kuroshio current system. In contrast, inshore squid hotspots are found within the CIP, namely in the Sunda Shelf Province, which may be linked to the occurrence of an ancient intermittent biogeographic barrier: a land bridge formed during the Pleistocene which severely restricted water flow between the Pacific and Indian Oceans, thereby facilitating squid fauna differentiation. Another marked pattern is a longitudinal richness cline from the Central (CIP) toward the Eastern Indo-Pacific (EIP) realm, with central Pacific archipelagos as evolutionary dead ends. In the Atlantic Ocean, closure of the Atrato Seaway (at the Isthmus of Panama) and Straits of Gibraltar (Mediterranean Sea) are historical processes that may explain the contemporary Caribbean octopus richness and Mediterranean sepiolid endemism, respectively. Last, we discuss how the life cycles and strategies of cephalopods may allow them to adapt quickly to future climate change and extend the borealization of their distribution.
Intertidal mangrove forests are a dynamic ecosystem experiencing rapid changes in extent and habitat quality over geological history, today and into the future. Climate and sea level have drastically altered mangrove distribution since their appearance in the geological record ∼75 million years ago (Mya), through to the Holocene. In contrast, contemporary mangrove dynamics are driven primarily by anthropogenic threats, including pollution, overextraction, and conversion to aquaculture and agriculture. Deforestation rates have declined in the past decade, but the future of mangroves is uncertain; new deforestation frontiers are opening, particularly in Southeast Asia and West Africa, despite international conservation policies and ambitious global targets for rehabilitation. In addition, geological and climatic processes such as sea-level rise that were important over geological history will continue to influence global mangrove distribution in the future. Recommendations are given to reframe mangrove conservation, with a view to improving the state of mangroves in the future.
Despite widespread climate-driven reductions of coral cover on tropical reefs, little attention has been paid to the possibility that changes in the geographic distribution of coral recruitment could facilitate beneficial responses to the changing climate through latitudinal range shifts. To address this possibility, we compiled a global database of normalized densities of coral recruits on settlement tiles (corals m-2) deployed from 1974 to 2012, and used the data therein to test for latitudinal range shifts in the distribution of coral recruits. In total, 92 studies provided 1253 records of coral recruitment, with 77% originating from settlement tiles immersed for 3-24 mo, herein defined as long-immersion tiles (LITs); the limited temporal and geographic coverage of data from short-immersion tiles (SITs; deployed for <3 mo) made them less suitable for the present purpose. The results from LITs show declines in coral recruitment, on a global scale (i.e. 82% from 1974 to 2012) and throughout the tropics (85% reduction at <20° latitude), and increases in the sub-tropics (78% increase at >20° latitude). These trends indicate that a global decline in coral recruitment has occurred since 1974, and the persistent reduction in the densities of recruits in equatorial latitudes, coupled with increased densities in sub-tropical latitudes, suggests that coral recruitment may be shifting poleward.
Algal assemblages are critical components of marine ecosystems from the intertidal to mesophotic depths; they act as primary producers, nutrient cyclers, and substrate providers. Coral reef ecosystems can be disrupted by stressors such as storm events, effluent inundation, sudden temperature shifts, and non-native invaders. Avrainvillea amadelpha is an invasive green alga that was first recorded in the main Hawaiian Islands on the west shore of Oahu and has continued to be of concern due to its extreme competitiveness with native algae and seagrasses. It has spread rapidly across the island of Oahu, decreasing the biodiversity of the benthos from shorelines to ∼90 m depth. We employed a boosted regression tree modeling framework to identify highly vulnerable regions prone to invasion. Our model indicated that regions exposed to minimal bottom currents and at least five degree heating weeks are particularly susceptible to A. amadelpha colonization. Additionally, we extrapolated our model to the main Hawaiian Islands and forecasted how a 25% increase in statewide annual maximum degree heating weeks may change habitat suitability for A. amadelpha. Across all islands, we identified particularly vulnerable “hotspot” regions of concern for resource managers and conservationists. This manuscript demonstrates the utility of this approach for identifying priority regions for invasive species management in the face of a changing climate.
On the basis of an analysis of recent reviews and other published sources, as well as the author’s unpublished data, an annotated checklist of fishes and fish-like animals found in the Russian waters of the northwestern Pacific Ocean at depths greater than 1000 m was compiled. The results show that 244 species of fishes and fish-like animals are currently recorded in this region representing 145 genera, 68 families and 24 orders. The most diverse by species are three families: Zoarcidae, Liparidae, and Myctophidae, which account for about 33% of all recorded species. The maximum number of species (230) was observed within the bathymetric range of 1000-2000 m, which is likely due to diurnal and seasonal vertical migrations of these species, for which the main habitat is the mesopelagial, upper continental slope and the adjacent lower shelf waters.