Robert John Toonen

University of Hawaiʻi at Mānoa | UH Manoa · Institute of Marine Biology

Hypotheses to explain chaotic genetic structure (i.e., a surprising degree of non-geographic temporal or spatial population differentiation) include: 1) variation in source of larval recruits, 2) self-recruitment and local subdivision, 3) variance in reproductive success (sweepstakes reproduction), and 4) pre- or post-settlement natural selection....

Marine biodiversity reaches its pinnacle in the tropical Indo-Pacific region, with high levels of both species richness and endemism, especially in coral reef habitats. While this pattern of biodiversity has been known to biogeographers for centuries, causal mechanisms remain enigmatic. Over the past 20 yrs, genetic markers have been employed by ma...

Coral reefs have great biological and socioeconomic value, but are threatened by ocean acidification, climate change and local human impacts. The capacity for corals to adapt or acclimatize to novel environmental conditions is unknown but fundamental to projected reef futures. The coral reefs of Kāne'ohe Bay, Hawai'i were devastated by anthropogeni...

Significance Although climate change is expected to decimate coral reefs, the combined impacts of ocean-warming and acidification on coral reef biodiversity remains largely unmeasured. Here, we present a two-year mesocosm experiment to simulate future ocean acidification and ocean-warming to quantify the impacts on species richness, community compo...

Major gaps remain in our understanding of the ecology, evolution, biodiversity, biogeography, extinction risk, and adaptive potential of reef building corals. One of the central challenges remains that there are few informative genetic markers for studying boundaries between species, and variation within species. Reduced representation sequencing a...

Marine heatwaves trigger severe coral bleaching events that result in dramatic losses of coral reefs worldwide. An increasingly common method used to mitigate coral bleaching is to shade portions of reefs. However, as shaded corals become less exposed to environmental stress, shading has also been hypothesized to lower their thermal tolerance, whic...

It is important to consider flow rate explicitly in coral growth and bleaching studies across multiple species with differing life histories to guide coral conservation, management and captive culture. We quantified growth rates and coral bleaching responses to thermal stress (approx. 18 DHW) in flow-through aquaria with various current velocities...

Coral reefs are among the most sensitive ecosystems affected by ocean warming and acidification, and are predicted to collapse over the next few decades. Reefs are predicted to shift from net accreting calcifier-dominated systems with exceptionally high biodiversity to net eroding algal-dominated systems with dramatically reduced biodiversity. Here...

Despite the dramatic decrease in high-throughput sequencing costs over time, sequencing the ideal number of individuals for population genetic inference remains prohibitively expensive. When research questions require only population-level resolution, pooling individual samples before sequencing (pool-seq) can substantially reduce costs while still...

Reef-building coral populations are at serious risk of collapse due to the combined effects of ocean warming and acidification. Nonetheless, many corals show potential to adapt to the changing ocean conditions. Here we examine the broad sense heritability (H ² ) of coral calcification rates across an ecologically and phylogenetically diverse sampli...

Under predicted future ocean conditions, corals will experience frequent and intense thermal stress events while simultaneously being exposed to chronic ocean acidification. Yet, some corals will likely be more resistant and/or resilient to these predicted conditions than others and may be critical to reef persistence in the future. Following natur...

Signals of natural selection can be quickly eroded in high gene flow systems, curtailing efforts to understand how and when genetic adaptation occurs in the ocean. This long‐standing, unresolved topic in ecology and evolution has renewed importance because changing environmental conditions are driving range expansions that may necessitate rapid evo...

Corals are early-branching animals highly reliant on diverse symbionts for growth and reproduction. Most coral groups, including stony corals and hydrocorals, exhibit deep genetic divergence between the Atlantic (ATO) and Indo-Pacific (IPO) oceans, hampering their direct comparison. Although sibling zoanthid species (Hexacorallia: Zoantharia) devia...

Climate-driven warming and changes in major ocean currents enable poleward transport and range expansions of many marine species. Here, we report the population genetic structure for the gastropod Kelletia kelletii , a commercial fisheries species and subtidal predator with top-down food web effects, whose populations have recently undergone climat...

Proteinase K (ProK) is regarded as an essential ingredient in most DNA extraction pro- tocols for protein-rich sample types such as tissue, blood, and mucus. However, ProK is expensive and may be unnecessary when samples are protein-limited, such as en- vironmental DNA (eDNA) from oligotrophic seawater. To investigate this, we filtered seawater thr...

Signals of natural selection can be quickly eroded in high gene-flow systems, severely challenging efforts to understand how and when genetic adaptation occurs in the ocean. This long-standing, unresolved topic in ecology has renewed importance because rapidly changing environmental conditions are driving range expansions that, in many cases, neces...

This study reports the first mitogenome from the antipatharian (black coral) genus Cirrhipathes (GenBank accession number ON653414). The 20,452 bp mitochondrial genome of Cirrhipathes cf. anguina LS-2022 consists of 13 protein-coding genes, two rRNA genes, and two tRNA genes (trnM and trnW). The mitogenome is typical of other antipatharian families...

Scleractinian corals are the main modern builders of coral reefs, which are major hot spots of marine biodiversity. Southern Atlantic reef corals are understudied compared to their Caribbean and Indo-Pacific counterparts and many hypotheses about their population dynamics demand further testing. We employed thousands of single nucleotide polymorphi...

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in e...

Understanding the genomic characteristics of non-model organisms can bridge research gaps between ecology and evolution. However, the lack of a reference genome and transcriptome for these species makes their study challenging. Here, we complete the first full genome and transcriptome sequence assembly of the non-model organism Kellet’s whelk, Kell...

The Gila robusta species complex in the lower reaches of the Colorado River includes three nominal and contested species (G. robusta, G. intermedia, and G. nigra) originally defined by morphological and meristic characters. In subsequent investigations, none of these characters proved diagnostic, and species assignments were based on capture locati...

The plasticity of some coral-associated microbial communities under stressors like warming and ocean acidification suggests the microbiome has a role in the acclimatization of corals to future ocean conditions. Here, we evaluated the acclimatization potential of coral-associated microbial communities of four Hawaiian coral species (Porites compress...

Seagrass habitats are declining worldwide, placing several seagrass‐associated animals at risk of extinction. The Critically Endangered limpet Siphonaria compressa is one of the rarest molluscs in Africa, and has been reported from only two disjunctive lagoons in South Africa. Being a highly specialized grazer that lives exclusively on the narrow b...

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in e...

The diversity and distribution of marine species in eastern Australia is influenced by one of the world's strongest western boundary currents, the East Australia Current, which propels water and propagules poleward, a flow intensifying due to climate change. Population genetic structure of the asterinid sea star Meridiastra calcar was investigated...

Coral reefs are iconic examples of climate change impacts because climate-induced heat stress causes the breakdown of the coral-algal symbiosis leading to a spectacular loss of color, termed ‘coral bleaching’. To examine the fine-scale dynamics of this process, we re-sampled 600 individually marked Montipora capitata colonies from across Kāne’ohe B...

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome‐scale genetic diversity data for wild p...

The gap between spawning and settlement location of marine fishes, where the larvae occupy an oceanic phase, is a great mystery in both natural history and conservation. Recent genomic approaches provide some resolution, especially in linking parent to offspring with assays of nucleotide polymorphisms. Here, the authors applied this method to the e...

Giant clams are ecologically important, benefitting species of all trophic levels. But numerous populations have declined drastically in numbers due to past intensive exploitation that led to their listing in both CITES Appendix II and IUCN Red List of Threatened Species. However, giant clams are notoriously difficult to identify, and recent molecu...

Giant clams are ecologically important, benefitting species of all trophic levels. But numerous populations have declined drastically in numbers due to past intensive exploitation that led to their listing in both CITES Appendix II and IUCN Red List of Threatened Species.. However, giant clams are notoriously difficult to identify, and recent molec...

Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studi...

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservat...

Fish have one of the highest occurrences of individual specialization in trophic strategies among Eukaryotes. Yet, few studies characterize this variation during trophic niche analysis, limiting our understanding of aquatic food web dynamics. Stable isotope analysis (SIA) with advanced Bayesian statistics is one way to incorporate this individual t...

The survival of most reef-building corals is dependent upon a symbiosis between the coral and the community of Symbiodiniaceae. Montipora capitata , one of the main reef-building coral species in Hawai'i, is known to host a diversity of symbionts, but it remains unclear how they change spatially and whether environmental factors drive those changes...

Traditional Hawaiian fishponds, called loko iʻa, are a low‐impact and culturally important aquaculture system that historically produced significant fish yields. To better understand the structure of the contemporary food web of the restored Heʻeia fishpond, a mark‐recapture experiment was conducted to estimate the population abundance of the three...

Successional theory proposes that fast growing and well dispersed opportunistic species are the first to occupy available space. However, these pioneering species have relatively short life cycles and are eventually outcompeted by species that tend to be longer-lived and have lower dispersal capabilities. Using Autonomous Reef Monitoring Structures...

Mesophotic coral ecosystems (MCEs: ~30 to 100+ m depth) may be older and more stable than shallow coral ecosystems that are more prone to disturbances in both the long term (glacial sea level cycles) and short term (heavy weather and anthropogenic activities). Here, we assess the phylogeography of two MCE fishes, the soldierfish Myripristis chryser...

The global decline of coral reefs has driven considerable interest in active coral restoration. Despite their importance and dominance on mature reefs, relatively few coral restoration projects use slower growth forms like massive and encrusting coral species. Micro-fragmentation can increase coral cover by orders of magnitude faster than natural g...

Our changing climate poses growing challenges for effective management of marine life, ocean ecosystems, and human communities. Which species are most vulnerable to climate change, and where should management focus efforts to reduce these risks? To address these questions, the National Oceanic and Atmospheric Administration (NOAA) Fisheries Climate...

Overview: Here we apply a a restriction-associated DNA sequencing approach (RAD-seq) to investigate the taxonomic classification of Tridacninae giant clams (genera: Hippopus and Tridacna) and address the phylogenetic discordance within the current literature, particularly in the subgenus Chametrachea. We compared mitochondrial and nuclear genomes t...

Our perception of reef diversity is dominated by corals, fish, and a few other groups that visibly dominate the reef surface. However, the bulk of reef biodiversity resides within the reef framework, and this cryptobiota is fundamentally important for the surface community. Sponges are abundant and conspicuous on the reef surface in productive, con...

Elevated seawater temperatures associated with climate change lead to coral bleaching. While the ultimate causes of bleaching are well understood, the proximate physiological mechanisms underlying the bleaching response are not as well defined. Here we measured nitric oxide synthase activity, oxidative stress, and cell death in algal symbionts (Sym...

Coral reefs are iconic examples of climate change impacts because climate-induced heat stress causes the breakdown of the coral-algal symbiosis leading to a spectacular loss of color, termed coral bleaching. To examine the fine-scale dynamics of this process, we re-sampled 600 individually marked Montipora capitata colonies from across Kāneohe Bay,...

Giant clams are keystone species on coral reefs, but global demand for their harvest has decimated populations and resulted in all Tridacnids being listed on both CITES and IUCN lists. However, giant clams are notoriously difficult to identify, and recent molecular work has revealed that morphological misidentification of giant clams have confounde...

The drastic decline in coral coverage has stimulated an interest in reef restoration, and various iterations of coral nurseries have been used to augment restoration strategies. Here we examine the growth of two species of Hawaiian Montipora that were maintained in mesocosms under either ambient or warmed annual bleaching conditions for two consecu...

Climate change poses a major threat to coral reefs. We conducted an outdoor 22-month experiment to investigate if coral could not just survive, but also physiologically cope, with chronic ocean warming and acidification conditions expected later this century under the Paris Climate Agreement. We recorded survivorship and measured eleven phenotypic...

Many marine animals have a biphasic life cycle in which demersal adults spawn pelagic larvae with high dispersal potential. An understanding of the spatial and temporal patterns of larval dispersal is critical for describing connectivity and local retention. Existing tools in oceanography, genetics, and ecology can each reveal only part of the over...

Novel methodologies now make it possible to track the complete geographical movements of seafood species from reproduction to human consumption. Doing so will better inform consumers and assist resource managers in matching fisheries and conservation policies with natural borders and pathways, including stock boundaries, networks of marine protecte...

The deep reef refuge hypothesis (DRRH) postulates that mesophotic coral ecosystems (MCEs) may provide a refuge for shallow coral reefs (SCRs). Understanding this process is an important conservation tool given increasing threats to coral reefs. To establish a better framework to analyze the DRRH, we analyzed stony coral communities in American Sāmo...

The survival of reef-building corals is dependent upon a symbiosis between the coral and the community of Symbiodiniaceae. Montipora capitata , one of the main reef building coral species in Hawaiʻi, is known to host a diversity of symbionts, but it remains unclear how they change spatially and whether environmental factors drive those changes. Her...

To evaluate potential coral adaptive mechanisms, we investigated physiological traits (biomass, lipid, protein, chlorophyll, and isotopic proxies for trophic strategy) in eight Hawaiian corals species along an environmental gradient of significant wave height, sea surface temperature, and seawater chlorophyll a concentration around the island of O‘...

The resistance of corals to a changing climate has been linked to physiological parameters including heterotrophic capacity and energy reserves. Recently, the potential flexibility and diversity of coral-associated microbial communities have also been related to coral health and resistance to environmental stress. This study uses the island of O‘ah...