About

Giacomo Bernardi is a researcher working on phylogeography, speciation, and molecular ecology of fishes. His research particularly focuses on fishes lacking a pelagic larval phase, with specific interest in species from the Sea of Cortez and the Pacific disjunct species, as well as surfperches (Embiotocidae). His work involves understanding the evolutionary history, biogeography, and genetic diversity of marine fishes, contributing to the broader knowledge of marine biodiversity and speciation processes.

Research topics

• Biology
• Ecology
• Data Mining
• Genetics
• Artificial Intelligence
• Computer Science
• Geology
• Oceanography
• Theoretical computer science
• Zoology
• Botany
• Paleontology
• Evolutionary biology
• Geography

Selected publications

• Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks

  PLoS ONE · 2021 · 14 citations

  Senior authorCorresponding
  • Computer Science
  • Data Mining
  • Artificial Intelligence

  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 metric, haplotype network branch diversity (HBd), as an easy way to quantifiably compare haplotype network complexity. Our metric builds off the logic of combining genetic and topological diversity to estimate complexity previously used by the published metric haplotype network diversity (HNd). However, unlike HNd which uses a combination of network features to produce complexity values that cannot be defined in probabilistic terms, thereby obscuring the values' implication for a sampled population, HBd uses frequencies of haplotype classes to incorporate topological information of networks, keeping the focus on the population and providing easy-to-interpret probabilistic values for randomly sampled individuals. The goal of this study is to introduce this more intuitive metric and provide an R script that allows researchers to calculate diversity and complexity indices from haplotype networks. A group of datasets, generated manually (model dataset) and based on published data (empirical dataset), were used to illustrate the behavior of HBd and both of its terms, haplotype diversity, and a new index called branch diversity. Results followed a predicted trend in both model and empirical datasets, from low metric values in simple networks to high values in complex networks. In short, the new combined metric joins genetic and topological diversity of haplotype networks, into a single complexity value. Based on our analysis, we recommend the use of HBd, as it makes direct comparisons of network complexity straightforward and provides probabilistic values that can readily discriminate situations that are difficult to resolve with available metrics.

  PublisherOA PDFDOI

• Comparative phylogeography of reef fishes indicates seamounts as stepping stones for dispersal and diversification

  Coral Reefs · 2021 · 25 citations

  • Ecology
  • Biology
  • Oceanography
  DOI

• Phylogeography of the banded butterflyfish, Chaetodon striatus, indicates high connectivity between biogeographic provinces and ecosystems in the western Atlantic

  Neotropical Ichthyology · 2020 · 12 citations

  Senior authorCorresponding
  • Biology
  • Ecology

  ABSTRACT 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, nothing is known about its phylogeography and how biogeographic barriers structure its populations. To assess the level of genetic connectivity among populations from distinct biogeographic provinces and environmental conditions, we collected samples from seven localities: Puerto Rico, in the Caribbean, and Tamandaré, Salvador, Abrolhos, Trindade Island, Arraial do Cabo and Florianópolis, in Brazil. One nuclear (rag 2) and two mitochondrial (control region and cyt b) molecular markers were sequenced. Our findings are consistent with a recent population expansion, around 30-120 thousand years ago, which was found for all populations. Haplotype network analyses point to the Caribbean as a refugium before the population expansion. Results show no geographic pattern of genetic diversity. Indeed, a lack of population structure was found and no isolation was observed across oceanographic barriers, as well as between coral and rocky reef ecosystems. Furthermore, no directionality in the migration pattern was found among populations. Since ecological and environmental characteristics are very diverse across such a vast geographic range, the lack of genetic differentiation suggests that C. striatus evolved ecological plasticity rather than local adaptation in the western Atlantic.

  DOI

• Distinct patterns of hybridization across a suture zone in a coral reef fish (<i>Dascyllus trimaculatus</i>)

  Ecology and Evolution · 2020 · 11 citations

  • Biology
  • Ecology
  • Zoology

  (Rüppell, 1829). Field observations indicate there are subtle color differences between Pacific and Indian Ocean lineages. Most importantly, population densities of color morphs and genetic analyses (mitochondrial DNA and SNPs obtained via RADSeq) suggest that the pattern of hybridization within the suture zone is not homogeneous. At CHR, both color morphs were present, mitochondrial haplotypes of both lineages were observed, and SNP analyses revealed both pure and hybrid genotypes. Meanwhile, in CKE, the Indian Ocean color morphs were prevalent, only Indian Ocean mitochondrial haplotypes were observed, and SNP analysis showed hybrid individuals with a large proportion (~80%) of their genotypes assigning to the Indian Ocean lineage. We conclude that CHR populations are currently receiving an influx of individuals from both ocean basins, with a greater influence from the Pacific Ocean. In contrast, geographically isolated CKE populations appear to be self-recruiting and with more influx of individuals from the Indian Ocean. Our research highlights how patterns of hybridization can be different at scales of hundreds of kilometers, due to geographic isolation and the history of interbreeding between lineages.

  DOI

Recent grants

• The impact of a large episodic disturbance on an invasive (outbreak) coral: Will Typhoon Maysak promote or suppress an invasive Montipora sp. Coral on reefs of Ulithi, Micronesia

  NSF · $166k · 2015–2018

Frequent coauthors

• Ricardo Beldade

  Pontificia Universidad Católica de Chile

  28 shared

• Serge Planes

  Université de Perpignan

  24 shared

• Gary C. Longo

  NOAA National Marine Fisheries Service Southwest Fisheries Science Center

  23 shared

• Giorgio Bernardi

  18 shared

• Sally J. Holbrook

  University of California, Santa Barbara

  16 shared

• Nicole L. Crane

  Society for Conservation Biology

  15 shared

• Ernesto Azzurro

  Institute for Marine Biological Resources and Biotechnology

  15 shared

• Giuseppe Bucciarelli

  University of California, Santa Cruz

  14 shared

Labs

• Bernardi LabPI

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