An integrated system to assess marine extinctions

More than 20 global marine extinctions and over 700 local extinctions have reportedly occurred during the past 500 years. However, available methods to determine how many of these species can be confidently declared true disappearances tend to be data-demanding, time-consuming, and not applicable to all taxonomic groups or scales of marine extinctions (global [G] and local [L]). We developed an integrated system to assess marine extinctions (ISAME) that can be applied to any taxonomic group at any geographic scale. We applied the ISAME method to 10 case studies to illustrate the possible ways in which the extinction status of marine species can be categorized as unverified, possibly extinct, or extinct. Of the 10 case studies we assessed, the ISAME method concludes that 6 should be categorized as unverified extinctions due to problems with species' identity and lack of reliable evidence supporting their disappearance (periwinkle-Littoraria flammea [G], houting-Coregonus oxyrinchus [G], long-spined urchin-Diadema antillarum [L], smalltooth sawfish-Pristis pectinata [L], and largetooth sawfish-P. pristis [L]). In contrast, ISAME classified the Guadalupe storm-petrel (Oceanodroma macrodactyla [G]) and the lost shark (Carcharhinus obsolerus [G]) as possibly extinct because the available evidence indicates that their extinction is plausible-while the largetooth sawfish [L] and Steller's sea cow (Hydrodamalis gigas [G]) were confirmed to be extinct. Determining whether a marine population or species is actually extinct or still extant is needed to guide conservation efforts and prevent further biodiversity losses.

Biopollution by Invasive Marine Non-Indigenous Species: A Review of Potential Adverse Ecological Effects in a Changing Climate

Biopollution by alien species is considered one of the main threats to environmental health. The marine environment, traditionally less studied than inland domains, has been the object of recent work that is reviewed here. Increasing scientific evidence has been accumulated worldwide on ecosystem deterioration induced by the development of massive non-indigenous population outbreaks in many coastal sites. Biopollution assessment procedures have been proposed, adopting criteria already used for xenochemical compounds, adjusting them to deal with alien species invasions. On the other hand, prevention and mitigation measures to reduce biopollution impact cannot always mimic the emission countermeasures that have been successfully applied for chemical pollutants. Nevertheless, in order to design comprehensive water-quality criteria, risk assessment and management strategies, based on scientific knowledge, have been developed in a similar way as for chemical pollution. The Mediterranean Sea is a well-known case of alien species invasion, mainly linked to the opening of the Suez Canal. Non-indigenous species have caused well-documented changes in many coastal ecosystems, favoured by concomitant changes induced by global warming and by the heavy load of nutrients and pollutants by various anthropogenic activities. Naval commercial traffic and leisure boats are among the most active vectors of spread for alien species inside the Mediterranean, and also towards other ocean regions. The scientific evidence gathered and summarized in this review suggests that effective management actions, under a precautionary approach, should be put in place in order to control introductions of species in new areas. These management measures are already established in international treaties and national legislations, but should be enforced to prevent the disruption of the dynamic ecological equilibria in the receiving environment and to control the direct adverse effects of alien species.

Coral mass mortalities in the Chagos Archipelago over 40 years: Regional species and assemblage extinctions and indications of positive feedbacks

The global decline of reef corals has been driven largely by several marine heatwaves. This has greatly reduced coral cover but has reduced coral diversity also. While there is a lack of data in most locations to detect coral species losses, reefs of the Chagos Archipelago, central Indian Ocean, have long term monitoring data extending back to the late 1970s. Severe declines in cover have occurred since the 1970s, with regional extinctions of some species and key species assemblages. There is a severe decline in coral settlement, along with a substantial loss of habitat quality which has reduced the habitat available for settlement. This is a clear precursor to positive feedback. Regional species extinctions here occur mainly when total coral cover is <10% of pre-warming levels. Climate models predict more frequent and more severe marine heatwaves, and even if this ecosystem recovers it will contain fewer species.

Replicated anthropogenic hybridisations reveal parallel patterns of admixture in marine mussels

Human-mediated transport creates secondary contacts between genetically differentiated lineages, bringing new opportunities for gene exchange. When similar introductions occur in different places, they provide informally replicated experiments for studying hybridisation. We here examined 4,279 Mytilus mussels, sampled in Europe and genotyped with 77 ancestry-informative markers. We identified a type of introduced mussels, called "dock mussels," associated with port habitats and displaying a particular genetic signal of admixture between M. edulis and the Mediterranean lineage of M. galloprovincialis. These mussels exhibit similarities in their ancestry compositions, regardless of the local native genetic backgrounds and the distance separating colonised ports. We observed fine-scale genetic shifts at the port entrance, at scales below natural dispersal distance. Such sharp clines do not fit with migration-selection tension zone models, and instead suggest habitat choice and early-stage adaptation to the port environment, possibly coupled with connectivity barriers. Variations in the spread and admixture patterns of dock mussels seem to be influenced by the local native genetic backgrounds encountered. We next examined departures from the average admixture rate at different loci, and compared human-mediated admixture events, to naturally admixed populations and experimental crosses. When the same M. galloprovincialis background was involved, positive correlations in the departures of loci across locations were found; but when different backgrounds were involved, no or negative correlations were observed. While some observed positive correlations might be best explained by a shared history and saltatory colonisation, others are likely produced by parallel selective events. Altogether, genome-wide effect of admixture seems repeatable and more dependent on genetic background than environmental context. Our results pave the way towards further genomic analyses of admixture, and monitoring of the spread of dock mussels both at large and at fine spacial scales.

Non-indigenous macrozoobenthic species on hard substrata of selected harbours in the Adriatic Sea

The intense shipping traffic characterising the Adriatic Sea favours the spread of marine organisms. Yet, a study of 12 Adriatic ports (4 on the western side and 8 on the eastern side of the basin) found that non-indigenous species (NIS) accounted for only 4% of the benthic communities settled on hard substrates. The cirripeds Amphibalanus amphitrite and Balanus trigonus, found in 8 harbours, were the most common invaders followed by Amphibalanus eburneus, the ascidian Styela plicata, and the bivalve Magallana gigas. The highest percentage of NIS was recorded in Venice and Ploče, the harbours with the least rich native communities; the lowest percentage was retrieved in Trieste, Koper, Pula, and Rijeka, the harbours hosting the highest species diversity. In contrast, the ports of Bari and Ancona showed both high NIS percentages and highly diversified communities.

Invasion dynamics of competing species with stage-structure

The spread of an invasive species often results in a decline and subsequent disappearance of native competitors. Several models, primarily based on spatially explicit Lotka-Volterra competition dynamics, have been developed to understand this phenomenon. In general, the goal of these models is to relate fundamental life history traits, for example dispersal ability and competition strength, to the rate of spread of the invasive species, which is also the rate at which the invasive species displaces its native competitor. Stage-structure is often an important determinant of population dynamics, but it has received little attention within the context of Lotka-Volterra invasion models. For many species, behaviors like dispersal and competition depend on life-stage. To describe the processes of invasion in these species, it is important to understand how behaviors that vary as a function of life-stage can impact spread rate. In this paper, we develop a spatially explicit, stage-structured Lotka-Volterra competition model. By comparing spread speed predictions from this model to spread speed predictions from an analogous single-stage model, we are able to determine when stage-structure is important and how stage-dependent behavior can alter the characteristics of an invasion.

Biodiversity: the known, unknown, and rates of extinction

How many species are there and how many have we lost? New estimates shed light on this question in the marine realm.

Spatial and temporal patterns of harvesting of the Vulnerable pig-nosed turtle Carettochelys insculpta in the Kikori region, Papua New Guinea

Management of wildlife use by communities living a partially traditional lifestyle is usually more successful when the interactions between those communities and the environment are well understood. We mapped the harvest areas for the Vulnerable pig-nosed turtle Carettochelys insculpta for six language-groups in the Kikori region of Papua New Guinea and compared harvest parameters between different areas and language-groups and, when possible, between 1980–1982 and 2007–2009. Spatially, the main influence on harvest method was a tribe's location relative to the turtle's distribution. No small juveniles (< 20 cm straight-line carapace length) were found outside the Kikori delta, which is probably the species’ feeding grounds. In contrast, nesting females were captured only in upstream and coastal sandbank areas. Temporally there were distinct differences in harvesting parameters between tribes, which may be explained by differential employment opportunities. To halt the decline of pig-nosed turtles in the Kikori region we recommend the establishment of beach and feeding-ground protection initiatives, together with monitoring of the turtle population and harvest. Concomitantly, trips specifically targeted at harvesting the turtles, which account for 81% of the animals captured, need to be restricted. These initiatives should include all six language-groups and take into account their specific harvesting patterns.

Shifting baselines and the extinction of the Caribbean monk seal

The recent extinction of the Caribbean monk seal Monachus tropicalis has been considered an example of a human-caused extinction in the marine environment, and this species was considered a driver of the changes that have occurred in the structure of Caribbean coral reef ecosystems since colonial times. I searched archaeological records, historical data, and geographic names (used as a proxy of the presence of seals) and evaluated the use and quality of these data to conclude that since prehistoric times the Caribbean monk seal was always rare and vulnerable to human predation. This finding supports the hypothesis that in AD 1500, the Caribbean monk seal persisted as a small fragmented population in which individuals were confined to small keys, banks, or isolated islands in the Gulf of Mexico and the Caribbean Sea. This hypothesis is contrary to the assumption that the species was widespread and abundant historically. The theory that the main driver of monk seal extinction was harvesting for its oil for use in the sugar cane industry of Jamaica during the 18th century is based primarily on anecdotal information and is overemphasized in the literature. An analysis of reported human encounters with this species indicates monk seal harvest was an occasional activity, rather than an ongoing enterprise. Nevertheless, given the rarity of this species and its restricted distribution, even small levels of hunting or specimen collecting must have contributed to its extinction, which was confirmed in the mid-20th century. Some sources had been overlooked or only partially reviewed, others misinterpreted, and a considerable amount of anecdotal information had been uncritically used. Critical examination of archaeological and historical records is required to infer accurate estimations of the historical abundance of a species. In reconstructing the past to address the shifting baseline syndrome, it is important to avoid selecting evidence to confirm modern prejudices.

Trends in the state of nature and their implications for human well-being

Two major international initiatives - the Convention on Biological Diversity's target to reduce the rate of biodiversity loss by 2010, and the Millennium Ecosystem Assessment - raise the profile of ecological data on the changing state of nature and its implications for human well-being. This paper is intended to provide a broad overview of current knowledge of these issues. Information on changes in the status of species, size of populations, and extent and condition of habitats is patchy, with little data available for many of the taxa, regions and habitats of greatest importance to the delivery of ecosystem services. However, what we do know strongly suggests that, while exceptions exist, the changes currently underway are for the most part negative, anthropogenic in origin, ominously large and accelerating. The impacts of these changes on human society are idiosyncratic and patchily understood, but for the most part also appear to be negative and substantial. Forecasting future changes is limited by our poor understanding of the cascading impacts of change within communities, of threshold effects, of interactions between the drivers of change, and of linkages between the state of nature and human well-being. In assessing future science needs, we not only see a strong role for ecological data and theory, but also believe that much closer collaboration with social and earth system scientists is essential if ecology is to have a strong bearing on policy makers.

Extinctions in ancient and modern seas

In the coming century, life in the ocean will be confronted with a suite of environmental conditions that have no analog in human history. Thus, there is an urgent need to determine which marine species will adapt and which will go extinct. Here, we review the growing literature on marine extinctions and extinction risk in the fossil, historical, and modern records to compare the patterns, drivers, and biological correlates of marine extinctions at different times in the past. Characterized by markedly different environmental states, some past periods share common features with predicted future scenarios. We highlight how the different records can be integrated to better understand and predict the impact of current and projected future environmental changes on extinction risk in the ocean.

Macroecology: does it ignore or can it encourage further ecological syntheses based on spatially local experimental manipulations? (American Society of Naturalists address)

Detailed natural history coupled to experimental ecology has provided a rich harvest of insights into how natural communities in all ecosystems function, insights that cannot be gleaned from macroecological analyses. That detail, generated by small-spatial-scale but often lengthy experiments, is essential to managing and even restoring ecosystems. My essay focuses primarily on the ecology of exposed rocky intertidal shores, but I believe the derived implications are generalizable to all ecosystems. A mainly experimental approach has tended to avoid a preoccupation with niches but instead has focused on the ecological roles exercised by particular species. Attention to roles has produced a growing appreciation for trophic cascades and their consequences, with obvious implications for the management of fisheries and the conservation significance of apex predators. Some studies are more phenomenological and others more reductionist in focus, but all provide pathways toward understanding abundance and body size variation or a miscellany of indirect effects. Microecology in all ecosystems should continue to prosper independently of a macroecological, predominately terrestrial perspective.

Biotic Homogenization of Inland Seas of the Ponto-Caspian

Comparative analysis of patterns of species invasion, dispersal, and impact on ecosystems in the Ponto-Caspian seas has been ongoing since 1900. The Black Sea is an important international shipping destination. High shipping intensity has facilitated species invasions into the Black Sea. Many species have successfully established because of Black Sea disturbances. The Black Sea serves as a hub for species that then spread further to the Sea of Azov, the Caspian Sea, the Sea of Marmara, and in some cases the eastern Mediterranean Sea. The Black Sea has thus become the main recipient for non-native species and acts as a donor to the seas of Eurasia. Native biodiversity has declined and invaders now dominate the Ponto-Caspian seas. This process has caused biotic homogenization of the Ponto-Caspian, as the same invaders determine community structure and in some cases ecosystem functioning in the different seas. Among these invaders, gelatinous species have become the main drivers of ecosystem functioning. The invasion rate of new species is accelerating.

Marine biodiversity in the Caribbean: regional estimates and distribution patterns

This paper provides an analysis of the distribution patterns of marine biodiversity and summarizes the major activities of the Census of Marine Life program in the Caribbean region. The coastal Caribbean region is a large marine ecosystem (LME) characterized by coral reefs, mangroves, and seagrasses, but including other environments, such as sandy beaches and rocky shores. These tropical ecosystems incorporate a high diversity of associated flora and fauna, and the nations that border the Caribbean collectively encompass a major global marine biodiversity hot spot. We analyze the state of knowledge of marine biodiversity based on the geographic distribution of georeferenced species records and regional taxonomic lists. A total of 12,046 marine species are reported in this paper for the Caribbean region. These include representatives from 31 animal phyla, two plant phyla, one group of Chromista, and three groups of Protoctista. Sampling effort has been greatest in shallow, nearshore waters, where there is relatively good coverage of species records; offshore and deep environments have been less studied. Additionally, we found that the currently accepted classification of marine ecoregions of the Caribbean did not apply for the benthic distributions of five relatively well known taxonomic groups. Coastal species richness tends to concentrate along the Antillean arc (Cuba to the southernmost Antilles) and the northern coast of South America (Venezuela-Colombia), while no pattern can be observed in the deep sea with the available data. Several factors make it impossible to determine the extent to which these distribution patterns accurately reflect the true situation for marine biodiversity in general: (1) highly localized concentrations of collecting effort and a lack of collecting in many areas and ecosystems, (2) high variability among collecting methods, (3) limited taxonomic expertise for many groups, and (4) differing levels of activity in the study of different taxa.

Depletion, Degradation, and Recovery Potential of Estuaries and Coastal Seas

Estuarine and coastal transformation is as old as civilization yet has dramatically accelerated over the past 150 to 300 years. Reconstructed time lines, causes, and consequences of change in 12 once diverse and productive estuaries and coastal seas worldwide show similar patterns: Human impacts have depleted >90% of formerly important species, destroyed >65% of seagrass and wetland habitat, degraded water quality, and accelerated species invasions. Twentieth-century conservation efforts achieved partial recovery of upper trophic levels but have so far failed to restore former ecosystem structure and function. Our results provide detailed historical baselines and quantitative targets for ecosystem-based management and marine conservation.

The role of marine reserves in achieving sustainable fisheries

Many fishery management tools currently in use have conservation value. They are designed to maintain stocks of commercially important species above target levels. However, their limitations are evident from continuing declines in fish stocks throughout the world. We make the case that to reverse fishery declines, safeguard marine life and sustain ecosystem processes, extensive marine reserves that are off limits to fishing must become part of the management strategy. Marine reserves should be incorporated into modern fishery management because they can achieve many things that conventional tools cannot. Only complete and permanent protection from fishing can protect the most sensitive habitats and vulnerable species. Only reserves will allow the development of natural, extended age structures of target species, maintain their genetic variability and prevent deleterious evolutionary change from the effects of fishing. Species with natural age structures will sustain higher rates of reproduction and will be more resilient to environmental variability. Higher stock levels maintained by reserves will provide insurance against management failure, including risk-prone quota setting, provided the broader conservation role of reserves is firmly established and legislatively protected. Fishery management measures outside protected areas are necessary to complement the protection offered by marine reserves, but cannot substitute for it.

Trawling and bottlenose dolphins' social structure

Human activities can affect the behaviour of mammals through the modification of habitats, changes in predation pressure or alterations in food distribution and availability. We analysed the association and ranging patterns of 242 individually identified bottlenose dolphins (Tursiops aduncus) in eastern Moreton Bay, Queensland, Australia, and distinguished two separate communities of dolphins. Unlike bottlenose dolphins elsewhere, the communities' core areas overlapped substantially. There was a correlation between the dolphins' responses to fishing activities and community membership-members of one community feed in association with trawlers and members of the other do not. Apart from feeding mode, the communities differed in habitat preference and group sizes. Inadvertent anthropogenic impacts on animals' societies are likely to be far more widespread than just this study and can increase conservation challenges. In this instance, managers need to consider the two communities' differing habitat requirements and their behavioural traditions in conservation planning.

What was natural in the coastal oceans?

Humans transformed Western Atlantic coastal marine ecosystems before modern ecological investigations began. Paleoecological, archeological, and historical reconstructions demonstrate incredible losses of large vertebrates and oysters from the entire Atlantic coast. Untold millions of large fishes, sharks, sea turtles, and manatees were removed from the Caribbean in the 17th to 19th centuries. Recent collapses of reef corals and seagrasses are due ultimately to losses of these large consumers as much as to more recent changes in climate, eutrophication, or outbreaks of disease. Overfishing in the 19th century reduced vast beds of oysters in Chesapeake Bay and other estuaries to a few percent of pristine abundances and promoted eutrophication. Mechanized harvesting of bottom fishes like cod set off a series of trophic cascades that eliminated kelp forests and then brought them back again as fishers fished their way down food webs to small invertebrates. Lastly, but most pervasively, mechanized harvesting of the entire continental shelf decimated large, long-lived fishes and destroyed three-dimensional habitats built up by sessile corals, bryozoans, and sponges. The universal pattern of losses demonstrates that no coastal ecosystem is pristine and few wild fisheries are sustainable along the entire Western Atlantic coast. Reconstructions of ecosystems lost only a century or two ago demonstrate attainable goals of establishing large and effective marine reserves if society is willing to pay the costs. Historical reconstructions provide a new scientific framework for manipulative experiments at the ecosystem scale to explore the feasibility and benefits of protection of our living coastal resources.

The evolutionary impact of invasive species

Since the Age of Exploration began, there has been a drastic breaching of biogeographic barriers that previously had isolated the continental biotas for millions of years. We explore the nature of these recent biotic exchanges and their consequences on evolutionary processes. The direct evidence of evolutionary consequences of the biotic rearrangements is of variable quality, but the results of trajectories are becoming clear as the number of studies increases. There are examples of invasive species altering the evolutionary pathway of native species by competitive exclusion, niche displacement, hybridization, introgression, predation, and ultimately extinction. Invaders themselves evolve in response to their interactions with natives, as well as in response to the new abiotic environment. Flexibility in behavior, and mutualistic interactions, can aid in the success of invaders in their new environment.

Collapse and recovery of marine fishes

Overexploitation and subsequent collapse of marine fishes has focused attention on the ability of affected populations to recover to former abundance levels and on the degree to which their persistence is threatened by extinction. Although potential for recovery has been assessed indirectly, actual changes in population size following long-term declines have not been examined empirically. Here I show that there is very little evidence for rapid recovery from prolonged declines, in contrast to the perception that marine fishes are highly resilient to large population reductions. With the possible exception of herring and related species that mature early in life and are fished with highly selective equipment, my analysis of 90 stocks reveals that many gadids (for example, cod, haddock) and other non-clupeids (for example, flatfishes) have experienced little, if any, recovery as much as 15 years after 45-99% reductions in reproductive biomass. Although the effects of overfishing on single species may generally be reversible, the actual time required for recovery appears to be considerable. To exempt marine fishes from existing criteria used to assign extinction risk would be inconsistent with precautionary approaches to fisheries management and the conservation of marine biodiversity.