Giacomo Bernardi

• Ph.D.
• Professor (Full) at University of California, Santa Cruz

In life sciences graduate programs in the United States, efforts are underway to address barriers to academic success—namely, using interventions targeted at addressing inclusivity and diversity concerns. However, graduate students are typically simultaneously workers for their institutions, where they face workplace challenges such as low wages, i...

Holacanthus angelfishes are some of the most iconic marine fishes of the Tropical Eastern Pacific (TEP). However, very limited genomic resources currently exist for the genus. In this study we: (i) assembled and annotated the nuclear genome of the King Angelfish (Holacanthus passer), and (ii) examined the demographic history of H. passer in the TEP...

Local and global ecological stressors are leading to increased documentation of phase shifts in coral reefs from healthy stony corals to macrophytes. In more rare cases, phase shifts result in sponge, zoantharian or other dominant species. In Ulithi Atoll, Federated States of Micronesia, we have documented an unusual phase shift from reefs with a d...

The rate of biological invasions is steadily increasing, with major ecological and economic impacts accounting for billions of dollars in damage as a result. One spectacular example is the western Atlantic invasion by lionfishes. In the Mediterranean Sea, invasions from the Red Sea via the Suez Canal (termed Lessepsian invasions) comprise more than...

The Regal Demoiselle, Neopomacentrus cyanomos is only the second Indo-Pacific reef fish (after the lionfish) to become well established in the Greater Caribbean (GC). It was first discovered, after it already was common, in the southwest Gulf of Mexico (SGM) in 2013. In 2019, an isolated second population was found at Trinidad, 3300 km away. The in...

Holacanthus angelfishes are some of the most iconic marine fishes of the Tropical Eastern Pacific (TEP). However, very limited genomic resources currently exist for the genus. In this study we: i) assembled and annotated the nuclear genome of the King Angelfish ( Holacanthus passer ), and ii) examined the demographic history of H. passer in the TEP...

Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure, and speciation (Dascyllus). The genus Dascyllus inclu...

The surfperches (family Embiotocidae) are a unique group of mostly marine fishes whose phylogenetic position within the Ovalentaria clade (Percomorpha) is still unresolved. As a result of their viviparity and lack of a dispersive larval stage, surfperches are an excellent model for the study of speciation, gene flow, and local adaptation in the oce...

Damselfishes (family Pomacentridae) comprise approximately 400 species that play an important ecological role in temperate and coral reefs. Here, for the first time, we assemble and annotate the mitochondrial genome of Dascyllus trimaculatus, the three-spot dascyllus, a planktivorous damselfish that primarily recruits in anemones. The circular geno...

Pricklebacks (Family Stichaeidae) are generally cold-temperate fishes most commonly found in the north Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Monkeyface Prickleback, Cebidichthys violaceus, to establish a genomic model for understanding phylogeographic patterns of marine organisms in...

Sculpins (Family Cottidae) are generally cold-temperate intertidal reef fishes most commonly found in the North Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Woolly Sculpin, Clinocottus analis, to establish a genomic model for understanding phylogeographic structure of inshore marine taxa al...

Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure and speciation ( Dascyllus ). The genus Dascyllus incl...

Surfperches (Family Embiotocidae) are viviparous temperate reef fishes that brood their young. This life history trait translates into limited dispersal, strong population structure, and an unusually strong potential for local adaptation in a marine fish. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the...

Keystone species are known to play a critical role in kelp forest health, including the well-known killer whales,sea otter,sea urchin,kelp trophic cascade in the Aleutian Islands, Alaska, USA. In California, a major player in the regulation of sea urchin abundance, and in turn, the health of kelp forests ecosystems, is a large wrasse, the Californi...

Acidification‐induced changes in neurological function have been documented in several tropical marine fishes. Here, we investigate whether similar patterns of neurological impacts are observed in a temperate Pacific fish that naturally experiences regular and often large shifts in environmental pH/pCO2. In two laboratory experiments, we tested the...

The Galápagos Archipelago is a place where terrestrial adaptive radiations of finches, mockingbirds, and tortoises have been studied extensively. In contrast, little is known about the potential for marine species to diverge among islands. The overall degradation of coral reefs in the Galápagos makes understanding the mechanisms and factors of spec...

Marine organisms that enter the Mediterranean from the Red Sea via the Suez Canal are known as Lessepsian bioinvaders. In general, genetic studies of Lessepsian fishes have shown little structure between Red Sea and Mediterranean populations. Yet notable exceptions suggest the importance of life-history factors that may influence patterns of spatia...

Marine organisms that enter the Mediter-ranean from the Red Sea via the Suez Canal are known as Lessepsian bioinvaders. In general, genetic studies of Lessepsian fishes have shown little structure between Red Sea and Mediterranean populations. Yet notable exceptions suggest the importance of life-history factors that may influence patterns of spati...

Studies on oceanic island biodiversity have been the foundation for much theoretical work. However, seamounts are mostly underexplored, and little information is available about their potential as stepping stones for oceanic dispersal and their role in diversification. Here we used a genetic approach to test different models of marine dispersal bet...

Acidification-induced changes in cognitive function and behavior have recently been documented in tropical marine fishes, raising concerns about related shifts in species interactions. Here, we investigate whether similar patterns of broad neurological impacts are observed in a temperate Pacific fish that experiences regular and often large shifts...

Despite increasing awareness of issues affecting inclusivity, equity and diversity, change has been slow in science and academia, and gender disparities remain significant. Biogeography has not escaped this pattern. Here, we present a virtual issue compiling some of the most cited papers led by women that have been published in the Journal of Bioge...

The diversity in the skeletal features of coral species is an outcome of their evolution, distribution and habitat. Here, we explored, from macro- to nano-scale, the skeletal structural and compositional characteristics of three coral species belonging to the genus Balanophyllia having different trophic strategies. The goal is to address whether th...

A common way of illustrating phylogeographic results is through the use of haplotype networks. While these networks help to visualize relationships between individuals, populations, and species, evolutionary studies often only quantitatively analyze genetic diversity among haplotypes and ignore other network properties. Here, we present a new metri...

Lessepsian fishes, entering the Mediterranean through the Suez Canal, have showed so far little genetic structure, but notable exceptions suggest the importance of life-history factors that may influence their patterns of spatial genetic variation. In this study, by sampling two invasive fishes with different life histories (the rabbitfish Siganus...

Nibblers (family Girellidae) are reef fishes that are mostly distributed in the Indo-Pacific, with one exception: Girella stuebeli, which is found in the Cabo Verde Archipelago, in the Atlantic Ocean. We capitalized on this unusual distribution to study the evolutionary history of the girellids, and determine the relationship between G. stuebeli an...

Here we present the first phylogeny of the genus Scartella based on mitochondrial data. The analysis strongly corroborates the validity of all species of the genus and shows that Scartella cristata, a species with a disjunct distribution, is a lineage complex comprising five clades: two in Caribbean waters, another in the East Atlantic/Mediterranea...

Abstract Hybrid zones are natural laboratories for investigating the dynamics of gene flow, reproductive isolation, and speciation. A predominant marine hybrid (or suture) zone encompasses Christmas Island (CHR) and Cocos (Keeling) Islands (CKE), where 15 different instances of interbreeding between closely related species from Indian and Pacific O...

Marine ecosystems are becoming increasingly altered worldwide as a result of human activities. The Mediterranean Sea is one of the most heavily impacted regions, facing unprecedented pressures including the spread of non-indigenous species. Monitoring of changes is therefore critical towards effective adoption of management measures. In this study,...

Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific pop...

Among the four butterflyfishes of the genus Chaetodon present in the western Atlantic, the banded butterflyfish Chaetodon striatus has the largest distribution range, spanning 44 degrees of latitude (from Massachusetts, USA to Santa Catarina, Brazil). Although the ecology of the banded butterflyfish has been well studied over its entire range, noth...

The distribution of marine life has been alarmingly reshaped lately and the number of non-indigenous species and their impacts are rapidly escalating globally. Timely and accurate information about the occurrence of non-indigenous species are of major importance for the mitigation of the issue. However, still large gaps in knowledge about marine bi...

We present a comprehensive review of the available global literature on the genetics and genomics of marine fish invasions. Overall this review provides data from 66 species belonging to 39 families, collected from 80 published studies on both WoS (Web of Science) and Scopus databases. We found that studies on alien fishes focused on specific geogr...

El pejeperro (Semicossyphus darwini) es una especie de labrido con un desarrollo hermafrodita protogénico que habita en los bosques de kelp de las costas del norte y centro norte de Chile. Esta especie, al igual que muchas otras especies de peces del submareal rocoso es fuertemente extraída por pescadores artesanales y buzos recreativos, sin ningun...

The evolution of parental care opens the door for the evolution of brood parasitic strategies that allow individuals to gain the benefits of parental care without paying the costs. Here we provide the first documentation for alloparental care in coral reef fish and we discuss why these patterns may reflect conspecific and interspecific brood parasi...

Islands are natural laboratories for evolution and biogeography studies. From MacArthur and Wil-son to present days, understanding processes such as dispersion, extinction, speciation and immigration is key to elucidate currents patterns of islands biogeography. However, these processes have been better investigated for terrestrial/aerial than for...

Population genetic analysis is an important tool for estimating the degree of evolutionary connectivity in marine organisms. Here, we investigate the population structure of the three-spot damselfish Dascyllus trimaculatus in the Red Sea, Arabian Sea and Western Indian Ocean, using 1174 single nucleotide polymorphisms (SNPs). Neutral loci revealed...

Genetic diversity is essential for species persistence because it provides the raw material for evolution. For marine organisms, short pelagic larval duration (PLD) and small population size are characteristics generally assumed to associate with low genetic diversity. The ecological diversity of organisms may also affect genetic diversity, with an...

On 5th November 2017, a puffer fish specimen was caught in the Aegean Sea. Morphological and molecular analysis identified it as Lagocephalus guentheri. This first record from Greek waters represents the westernmost observation of the species in the Mediterranean Sea. The expansion and establishment of puffer fish species in the basin are discussed...

Embiotocidae, a unique family within the Perciformes that has evolved a complex viviparous natural history, has lacked full resolution and strong support in several interspecific relationships until recently. Here we propose three taxonomic revisions within embiotocid surfperches based on recent molecular phylogenetic analyses that robustly resolve...

The Hawaiian Archipelago, one of the most remote archipelagoes in the world, is a hotspot for reef fish endemism. The restricted biogeographic range sizes of endemic species have been interpreted to indicate low dispersal ability, whereas broad distributions of widespread species are assumed to indicate high dispersal potential. To assess that intu...

The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, prec...

Estimating population sizes and genetic diversity are key factors to understand and predict population dynamics. Marine species have been a difficult challenge in that respect, due to the difficulty in assessing population sizes and the open nature of such populations. Small, isolated islands with endemic species offer an opportunity to groundtruth...

Density (number per m2) from visual census for Holacanthus limbaughi and Stegastes baldwini by depth. Data shown as box plots by depth, shallow (6–12 m) and deep (20m). (PDF)

Bathymetric map of Clipperton Atoll that shows habitat estimated contours. Pink outline represents the 50 m “shallow” water, blue outline respesents the 100m “deep” water. Numbers on the map represent depths values in fathoms. (PDF)

Picture of a group of Holacanthus limbaughi taken from a submersible dive at 110 m depth in 2016 (Alan Friedlander). (JPG)

Barcode split perl script. (TXT)

Density (number per m2) from visual census for Holacanthus limbaughi and Stegastes baldwini by year. Data shown as box plots by year of census. (PDF)

Quality filtering perl script. (TXT)

iSea launched in 2016 a citizen science project aiming at improving our knowledge on marine Non-Indigenous species in Greece

To date, the Mediterranean Sea has been subjected to numerous non-indigenous species’ introductions raising the attention of scientists, managers, and media. Several introduction pathways contribute to these introduction, including Lessepsian migration via the Suez Canal, accounting for approximately 100 fish species, and intentional or non-intenti...

Group-living animals commonly display differences in behaviour, physiology and endocrine profiles between conspecifics within the group, which are tightly linked to reproduction. Teleosts exhibit a variety of social systems, where social status, as well as sex, has been linked to different androgen and oestrogen profiles. Levels of gonadal androgen...

Following aquarium releases, invasive lion shes have colonized large areas of the Caribbean and western Atlantic, resulting in an immense ecological damage. The early stages of that invasion are poorly known. Indeed, a lag of time between the introduction and detection often preclude genetic characterization of that crucial phase. With elevated awa...

Recently, tilapia have become increasingly important in aquaculture and fisheries worldwide. They are one of the major protein sources in many African countries and are helping to combat malnutrition. Therefore, maintenance and conservation genetics of wild populations of tilapia are of great significance. In this study, we report the population ge...

Indigenous people, despite their pivotal roles in linking knowledge with contemporary needs and economies, have not always been acknowledged for their input. Professionally trained scientists and conservationists, rather than working with local people as key collaborators and data collectors, often attempt to enlist the support of local people to i...

Studies on the distribution and evolution of organisms on oceanic islands have advanced towards a dynamic perspective1, where terrestrial endemicity results from island geographical aspects and geological history2 intertwined with sea-level fluctuations3,4. Diversification on these islands may follow neutral models5, decreasing over time as niches...

on the occasion of the 10th Indo-Pacific Fish Conference (http://ipfc10.criobe.pf/) to be held in Tahiti in October 2017, it seemed timely to update Randall’s 1985 list of the fishes known from French Polynesia. Many studies focusing on fishes in this area have been published since 1985, but Randall’s list remains the authoritative source. Herein w...

A new species of damselfish, Altrichthys alelia sp. n. is described from specimens collected in shallow water (1–8m depth) off Busuanga Island, Palawan Province, Philippines. It differs from the other two species in the genus, A. curatus and A. azurelineatus, in various features including having golden upper body lacking dark edges of dorsal and ca...

The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reef...

Number of benthic quadrats examined for all years and all sites. (DOCX)

Functional group definitions for benthic community structure. (DOCX)

Fish species observed on Ulithi Atoll fish transects 2012–2014 with trophic group designations. (DOCX)

Out of more than 380 species of damselfish, only three lack a pelagic larval phase, Acanthochromis polyacanthus, that ranges from the Philippines to the Great Barrier Reef, and two species in the genus Altrichthys, A. azurelineatus and A. curatus, that are restricted to the Calamian Archipelago (Palawan province) in the Philippines. Therefore in a...

In the California Current ecosystem, global climate change is predicted to trigger large-scale changes in ocean chemistry within this century. Ocean acidification—which occurs when increased levels of atmospheric CO2 dissolve into the ocean—is one of the biggest potential threats to marine life. In a coastal upwelling system, we compared the effect...

Summary of copper rockfish (Sebastes caurinus) Trinity de novo assembly and BLAST annotations. (PDF)

Blue rockfish differentially expressed (DE) genes grouped by heatmap cluster (Fig 3A), including manual annotation (category) based on gene ontology classification and primary literature review, Uniprot gene description, accession and e-value, maximum fold change, Trinity contig, and whether the Uniprot Accession was significant in both species. Th...

Copper rockfish differentially expressed (DE) genes grouped by heatmap cluster (Fig 3A), including manual annotation (category) based on gene ontology classification and primary literature review, Uniprot gene description, accession and e-value, maximum fold change, Trinity contig, and whether the Uniprot Accession was significant in both species....

Routine metabolic rate and maximum metabolic rate of copper and blue rockfish. (A,B) Routine metabolic rate was measured as the oxygen consumption rate while at rest. (C,D) Maximum metabolic rate was measured as the oxygen consumption rate calculated while the fish swam at its presumed maximum rate in a swim tunnel. Letters over bars represent resu...

Principal component analysis using an unsupervised analysis of all gene transcripts. Treatment groupings are similar to those observed in the heatmaps for differentially expressed gene patterns (Fig 3). A) For copper rockfish, PC2 (12.9%) and PC3 (11.6%) separated pCO2 treatments into the two highest and lowest pCO2 treatments. The variance explain...

Gene Ontology (GO) consortium accession numbers from Fig 2B in the main text. (PDF)

Absolute lateralization index (higher values are more lateralized) for copper and blue rockfish as a function of pCO2 treatment history. Bars are mean values (± SE). Letters over bars represent results of Tukey HSD post-hoc tests; significantly different means do not share letters in common. (PDF)

pH time series (A) from Carmel Bay, California collected using a SeaFET sensor (with a Durafet ISFET pH electrode) deployed to the benthos in the center of a large kelp bed at 12 m depth (B). pH readings were made every 15 minutes and are plotted as hourly means. The gap from May to October 2013 occurred due to a flooded housing. (PDF)

Growth rates (mm d-1) measured as a change in length over the experimental exposure duration for copper and blue rockfish as a function of pCO2 treatment history. Bars are mean values (± SE). Letters over bars represent results of Tukey HSD post-hoc tests; significantly different means do not share letters in common. (PDF)

Molecular function and biological process Gene Ontology (GO) categories represented in the annotated copper rockfish de novo transcriptome assembly. Compared to the full assembly, differentially expressed genes (Fig 3B) showed increased expression of genes involved in transcription activity and biological regulation in copper rockfish and increased...

The Western Indian Ocean harbors one of the world’s most diverse marine biota yet is threatened by exploitation with few conservation measures in place. Primary candidates for conservation in the region are the Scattered Islands (Îles Éparses), a group of relatively pristine and uninhabited islands in the Mozambique Channel. However, while optimal...

Oceanographic features influence the transport and delivery of marine larvae, and physical retention mechanisms, such as eddies, can enhance self-recruitment (i.e., the return of larvae to their natal population). Knowledge of exact locations of hatching (origin) and settlement (arrival) of larvae of reef animals provides a means to compare observe...

RESEARCH ARTICLE Corallimorph and Montipora Reefs in Ulithi Atoll, Micronesia: documenting unusual reefs Nicole L. Crane, Michelle J. Paddack, Peter A. Nelson, Avigdor Abelson, John Rulmal, Jr. & Giacomo Bernardi Abstract Here we report the presence of two unusual reef types at Ulithi Atoll, Yap State, Federated States of Micronesia: 1. a coral...

Biological invasions are increasingly creating ecological and economical problems both on land and in aquatic environments. For over a century, the Mediterranean Sea has steadily been invaded by Indian Ocean / Red Sea species (called Lessepsian invaders) via the Suez Canal, with a current estimate of approximately 450 species. The bluespotted corne...

Endemic marine species at remote oceanic islands provide opportunities to investigate the proposed correlation between range size and dispersal ability. Because these species have restricted geographic ranges, it is assumed that they have limited dispersal ability, which consequently would be reflected in high population genetic structure. To asses...