Nancy Knowlton

Smithsonian Institution

Aim As anthropogenic stressors on the biosphere intensify, understanding how communities respond to disturbances is critical. Biodiversity is often thought to promote the stability of communities over time and enhance ecosystem functioning. However, results have been inconsistent, and the multifaceted linkages among diversity, stability and functio...

The search for ways to protect and restore ocean health is rapidly accelerating and expanding. A new collection of articles draws on biological and social sciences to suggest changes in how ocean science and conservation are conducted to achieve a sustainable, healthy and inclusive future.

The ocean is facing multiple pressures from human activities, including the effects of climate change. Science has a prominent role in identifying problems and communicating these to society. However, scientists are also increasingly taking an active role in developing solutions, including strategies for adapting to and mitigating climate change, i...

Analysis of environmental DNA is increasingly used to characterize ecological communities, but the effectiveness of this approach depends on the accuracy of taxonomic reference databases. The MIDORI databases, first released in 2017, were built to improve accuracy for mitochondrial metazoan (animal) sequences. MIDORI has now been significantly impr...

Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across depth...

Small cryptic invertebrates (the cryptofauna) are extremely abundant, ecologically important, and species rich on coral reefs. Ongoing ocean acidification is likely to have both direct effects on the biology of these organisms, as well as indirect effects through cascading impacts on their habitats and trophic relationships. Naturally acidified hab...

Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea, and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across dept...

this document is the work of a team assembled by the International Coral Reef Society (ICRS). The mission of ICRS is to promote the acquisition and dissemination of scientific knowledge to secure the future of coral reefs, including via relevant policy frameworks and decision-making processes. This document seeks to highlight the urgency of taking...

Impacts of marine heatwaves are worse when seaweeds and sea urchins are abundant

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03271-2.

Background The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic gr...

Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama Abstract The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event h...

While the ocean has suffered many losses, there is increasing evidence that important progress is being made in marine conservation. Examples include striking recoveries of once-threatened species, increasing rates of protection of marine habitats, more sustainably managed fisheries and aquaculture, reductions in some forms of pollution, accelerati...

Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition. We tested whether a single PCR survey of eDNA in seawater using a broad...

Sustainable Development Goal 14 of the United Nations aims to “conserve and sustainably use the oceans, seas and marine resources for sustainable development”. Achieving this goal will require rebuilding the marine life-support systems that deliver the many benefits that society receives from a healthy ocean. Here we document the recovery of marine...

The rapid anthropogenic climate change that is being experienced in the early twenty-first century is intimately entwined with the health and functioning of the biosphere. Climate change is impacting ecosystems through changes in mean conditions and in climate variability, coupled with other associated changes such as increased ocean acidification...

Traditional methods of characterizing biodiversity are increasingly being supplemented and replaced by approaches based on DNA sequencing alone. These approaches commonly involve extraction and high-throughput sequencing of bulk samples from biologically complex communities or samples of environmental DNA (eDNA). In such cases, vouchers for individ...

Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition, but most studies to date have evaluated its effectiveness in single habi...

A decision framework for implementation of possible interventions.

Theories involving niche diversification to explain high levels of tropical diversity propose that species are more likely to co‐occur if they partition at least one dimension of their ecological niche space. Yet, numerous species appear to have widely overlapping niches based upon broad categorizations of resource use or functional traits. In part...

Interventions to increase the resilience and persistence of coral reefs.

Sponges act as important microhabitats in the marine environment and promote biodiversity by harboring a wide variety of macrofauna, but little is known about the magnitude and patterns of diversity of sponge-associated communities. This study uses DNA barcoding to examine the macrofaunal communities associated with Stylissa carteri in the central...

Earth Optimism—recapturing the positive - Volume 53 Issue 1 - Nancy Knowlton

The introduction of non-native rats can devastate island ecosystems. It now emerges that these rats also harm a complex web of interactions linking seabirds with the algae and fishes of nearby coral reefs. The introduction of non-native rats can devastate island ecosystems. It now emerges that these rats also harm a complex web of interactions link...

Coral reef ecosystems are seriously threatened by changing conditions in the ocean. Although many factors are implicated, climate change has emerged as a dominant and rapidly growing threat. Developing a long‐term strategic plan for the conservation of coral reefs is urgently needed yet is complicated by significant uncertainty associated with clim...

Coral reefs harbor diverse assemblages of organisms yet the majority of this diversity is hidden within the three dimensional structure of the reef and neglected using standard visual surveys. This study uses Autonomous Reef Monitoring Structures (ARMS) and amplicon sequencing methodologies, targeting mitochondrial cytochrome oxidase I and 18S rRNA...

Coastal oceans are increasingly eutrophic, warm and acidic through the addition of anthropogenic nitrogen and carbon, respectively. Among the most sensitive taxa to these changes are scleractinian corals, which engineer the most biodiverse ecosystems on Earth. Corals' sensitivity is a consequence of their evolutionary investment in symbiosis with t...

Mutually beneficial interactions between species (mutualisms) shaped the evolution of eukaryotes and remain critical to the survival of species globally [1, 2]. Theory predicts that hosts should pass mutualist symbionts to their offspring (vertical transmission) [3-8]. However, offspring acquire symbionts from the environment in a surprising number...

Target 14 of the Global Strategy for Plant Conservation calls for an increase in the communication of the importance of plant diversity and conservation by education and public awareness programs. An unrelenting torrent of bad news about the environment and the loss of plant biodiversity, however, have led to despair among conservation practitioner...

Coral reefs are the most biodiverse marine ecosystems on the planet, with at least one quarter of all marine species associated with reefs today. This diversity, which remains very poorly understood, is nevertheless extraordinary when one considers the small proportion of ocean area that is occupied by coral reefs. Networks of competitive and troph...

Anthropogenic habitats are increasingly prevalent in coastal marine environments. Previous research on sessile epifauna suggests that artificial habitats act as a refuge for nonindigenous species, which results in highly homogenous communities across locations. However, vertebrate assemblages that live in association with artificial habitats are po...

Scientific Reports 7 : Article number: 44923 10.1038/srep44923 ; published online: 30 March 2017 ; updated: 16 May 2017 This Article contains typographical errors in Table 2. For Gene ‘COI’, species ‘ T. guttata ’ under ‘Present study’, the location ‘RI’ should read ‘RI, NC’.

A focus on conservation in this issue of Science appears on the eve of Earth Day, which is being celebrated by scientists in meetings and public events worldwide. Conservation professionals, who have long condemned attacks on the environment, will gather for Earth Optimism events to highlight conservation achievements. Separately, but simultaneousl...

The best way to encourage conservation is to share our success stories, not to write obituaries for the planet, says Nancy Knowlton.

Several obligate associate crabs and shrimps species may co-occur and interact within a single coral host, leading to patterns of associations that can provide essential ecological services. However, knowledge of the dynamics of interactions in this system is limited, partly because identifying species involved in the network remains challenging. I...

DNA metabarcoding, the PCR-based profiling of natural communities, is becoming the method of choice for biodiversity monitoring because it circumvents some of the limitations inherent to traditional ecological surveys. However, potential sources of bias that can affect the reproducibility of this method remain to be quantified. The interpretation o...

List of specimens, including taxonomy and GenBank accession numbers, that were tissue subsampled to make up the mock sample Specimens are ranked based on the proportion of sequences recovered in the metabarcoding dataset.

Sample by observation contingency table displaying the number of reads per OTU and per sample

Phylogenetic relationships between representative COI sequences (313 bp) of 120 OTUs detected in the mock sample estimated using a Maximum Likelihood approach We used a general time reversible nucleotide model with a proportion of invariant sites and among site rate heterogeneity modeled with a discrete gamma distribution (GTR +I +G) together with...

COI amplicon data analysis script

Effect of rarefaction subsampling on the reproducibility of beta diversity The OTU table was rarefied five times down to the lowest number of sequences that a sample contained (45,609). See Table 2 for a summary of pairwise dissimilarity calculations.

Significance Oxygen-starved coastal waters are rapidly increasing in prevalence worldwide. However, little is known about the impacts of these “dead zones” in tropical ecosystems or their potential threat to coral reefs. We document the deleterious effects of such an anoxic event on coral habitat and biodiversity, and show that the risk of dead-zon...

Mitochondrial-encoded genes are increasingly targeted in studies using high-throughput sequencing approaches for characterizing metazoan communities from environmental samples (e.g., plankton, meiofauna, filtered water). Yet, unlike nuclear ribosomal RNA markers, there is to date no high-quality reference dataset available for taxonomic assignments...

Massive coral bleaching events associated with high sea surface temperatures are forecast to become more frequent and severe in the future due to climate change. Monitoring colony recovery from bleaching disturbances over multiyear time frames is important for improving predictions of future coral community changes. However, there are currently few...

Many conservation strategies identify a narrow subset of genotypes, species, or geographic locations that are predicted to be favored under different scenarios of future climate change. However, a focus on predicted winners, which might not prove to be correct, risks undervaluing the balance of biological diversity from which climate-change winners...

Large environmental fluctuations often cause mass extinctions, extirpating species and transforming communities [1, 2]. While the effects on community structure are evident in the fossil record, demographic consequences for populations of individual species are harder to evaluate because fossils reveal relative, but not absolute, abundances. Howeve...

Lobophylliidae is a family-level clade of corals within the ‘robust’ lineage of Scleractinia. It comprises species traditionally classified as Indo-Pacific ‘mussids’, ‘faviids’, and ‘pectiniids’. Following detailed revisions of the closely related families Merulinidae, Mussidae, Montastraeidae, and Diploastraeidae, this monograph focuses on the tax...

The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of d...

A study led by researchers from the University of Jordan and the Smithsonian Institution reports the first survey of the typically overlooked cryptic organisms found on reefs of the Jordanian coast of the Gulf of Aqaba (Northern Red Sea) using a standardized sampling protocol and high-throughput DNA barcoding (metabarcoding).

The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true wou...

High-Throughput Sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs o...

PCR amplification followed by deep sequencing of homologous gene regions is increasingly used to characterize the diversity and taxonomic composition of marine eukaryotic communities. This approach may generate millions of sequences for hundreds of samples simultaneously. Therefore, tools that researchers can use to visualize complex patterns of di...

Bacon et al. (1) “reject a 3.5 Ma assumption” for the closure of the Central American Seaway, a conclusion that echoes earlier studies that established that the “bulk [of marine ‘geminate’ or ‘transisthmian’ species on opposite sides of the Isthmus] were split at some point during the long period of geological upheavals associated with the rising I...

The header “Forward primers (3' to 5')” should read “Forward primers (5' to 3'),” and the header “Reverse complement primers (3' to 5’)” should read “Reverse complement primers (5' to 3’).” The authors have provided a corrected version of Table 1 here. Table 1 List of the 18S and 28S ribosomal DNA primers designed in this study.

Many cnidarians host endosymbiotic dinoflagellates from the genus Symbiodinium. It is generally assumed that the symbiosis is mutualistic, where the host benefits from symbiont photosynthesis while providing protection and photosynthetic substrates. Diverse assemblages of symbiotic gorgonian octocorals can be found in hard bottom communities throug...

We describe Symbiodinium necroappetens sp. nov. found predominantly in diseased or thermally damaged tissues in some reef corals of the Greater Caribbean. Small, albeit fixed, differences in the ribosomal DNA (ITS2 and LSU) and cytochrome b (cob) indicate that S. necroappetens is evolutionarily separate, but closely related to S. microadriaticum (m...

Significance High-throughput DNA sequencing methods are revolutionizing our ability to census communities, but most analyses have focused on microbes. Using an environmental DNA sequencing approach based on cytochrome c oxidase subunit 1 primers, we document the enormous diversity and fine-scale geographic structuring of the cryptic animals living...

Global species richness, whether estimated by taxon, habitat, or ecosystem, is a key biodiversity metric. Yet, despite the global importance of biodiversity and increasing threats to it (e.g., [1-4]), we are no better able to estimate global species richness now than we were six decades ago [5]. Estimates of global species richness remain highly un...

The tools of molecular genetics have been transformed over the last decades and have in turn transformed our understanding of coral reefs. Initially limited to information on single genes, we are now capable of analyzing entire genomes. These developments make it possible to do many things that were either impossible or extremely difficult before:...

We examined the long-term reproductive consequence of bleaching stress on Caribbean corals in the Orbicella (formerly Montastraea) species complex (O. annularis, O. faveolata and O. franksi). Over 2000 observations of spawning in 526 tagged corals in Panama were made from 2002 through 2013. Bleaching events were noted in 2005 and 2010. At the popul...

Modern coral taxonomy has begun to resolve many long-standing problems in traditional systematics stemming from its reliance on skeletal macromorphology. By integrating examinations of colony, corallite, and subcorallite morphology with the molecular sequence data that have proliferated in the last decade, many taxa spread across the scleractinian...

Explaining patterns of commonness and rarity is fundamental for understanding and managing biodiversity. Consequently, a key test of biodiversity theory has been how well ecological models reproduce empirical distributions of species abundances. However, ecological models with very different assumptions can predict similar species abundance distrib...