Santiago Herrera

Santiago Herrera
Lehigh University

PhD

About

75
Publications
31,046
Reads
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1,750
Citations
Additional affiliations
August 2016 - May 2020
Lehigh University
Position
  • Professor (Assistant)
March 2015 - August 2016
University of Toronto
Position
  • PostDoc Position
June 2009 - December 2014
Massachusetts Institute of Technology
Position
  • Research Assistant
Education
June 2009 - December 2014
Woods Hole Oceanographic Institution
Field of study
  • Biological Oceanography
June 2009 - December 2014
Massachusetts Institute of Technology
Field of study
  • Biological Oceanography
June 2007 - May 2009
Los Andes University (Colombia)
Field of study
  • Biological Sciences

Publications

Publications (75)
Article
Full-text available
The distributions of anthozoan corals are undercharacterized due to their wide bathymetric ranges, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a noninvasive strategy to complement conventional approaches for mapping and monitoring the distribution and bi...
Article
Full-text available
A new family of antipatharian corals, Ameripathidae (Cnidaria: Anthozoa: Antipatharia), is established for Ameripathes pseudomyriophylla Opresko & Horowitz, gen. et sp. nov. The new family resembles Myriopathidae and Stylopathidae in terms of the morphology of the polyps and tentacles and the pinnulate branching of the corallum. Phylogenetic analys...
Article
Full-text available
Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low‐coverage genome sequencing) is a promising method to not only extract high‐copy loci but also 100s to 1000s of phylogenetically...
Conference Paper
Full-text available
Ecosystems are linked by the movement of organisms across habitat boundaries. Effective ecosystem-based fisheries management relies on an understanding of how these movements change both as part of natural ontogenetic shifts and in response to environmental stressors. As part of the Connectivity of Coral Ecosystems in the Northwestern Gulf of Mexic...
Article
Full-text available
Reactive oxygen species (ROS) are central to diverse biological processes through which organisms respond to and interact with their surroundings. Yet, a lack of direct measurements limits our understanding of the distribution of ROS in the ocean. Using a recently developed in situ sensor, we show that deep-sea corals and sponges produce the ROS su...
Preprint
Full-text available
The distributions of anthozoan corals are under-characterized due to their wide bathymetric range, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a non-invasive strategy to complement conventional approaches for mapping and monitoring coral communities. Pri...
Preprint
Full-text available
1: Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage whole genome sequencing) remains a low-cost, promising method to not only extract high-copy loci, but also 100s to 1...
Preprint
Coral-associated microbiomes vary greatly between coral colonies and sampling locations with functional consequences on the coral host. However, the full extent of variability across the ranges of most coral species remains unknown, especially in octocorals and species from mesophotic and deep-sea habitats. Here we characterized the microbiomes of...
Article
Full-text available
Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated Pac...
Preprint
Full-text available
Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated Pac...
Article
Full-text available
Volcanic eruptions provide rare opportunities to witness the biological recolonization of areas covered by new lava flows by effectively resetting the ecological succession clock to zero. The role of submarine volcanic eruptions as disturbance events and the resulting patterns of ecological succession have mainly been studied in hydrothermal vent e...
Article
Full-text available
The ocean’s vast twilight, or mesopelagic, zone (200–1,000 m depth) harbors immense biomass consisting of myriad poorly known and unique animal species whose quantity and diversity are likely considerably underestimated. As they facilitate the movement of carbon from surface waters to the deep sea through feeding and migratory behaviors, ocean twil...
Article
Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the...
Article
Full-text available
Comprehensive knowledge of the distribution of active hydrothermal vent fields along midocean ridges is essential to understanding global chemical and heat fluxes and endemic faunal distributions. However, current knowledge is biased by a historical preference for on-axis surveys. A scarcity of high-resolution bathymetric surveys in off-axis region...
Article
Full-text available
Environmental DNA (eDNA) quantification and sequencing are emerging techniques for assessing biodiversity in marine ecosystems. Environmental DNA can be transported by ocean currents and may remain at detectable concentrations far from its source depending on how long it persist. Thus, predicting the persistence time of eDNA is crucial to defining...
Article
Full-text available
The processes that control diversification and speciation in deep-sea species are poorly known. Here, we analyzed data produced by Restriction-Site Associated DNA Sequencing (RAD-Seq) of octocorals in the genus Paramuricea to elucidate diversification patterns and examine the role of environmental gradients in their evolution. The genus Paramuricea...
Preprint
Full-text available
Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the...
Article
Full-text available
Fine-scale larval dispersal and connectivity processes are key to species survival, growth, recovery and adaptation under rapidly changing disturbances. Quantifying both are required to develop any effective management strategy. In the present work, we examine the dispersal pattern and potential connectivity of a common deep-water coral, Paramurice...
Article
Full-text available
The degree of connectivity among populations influences their ability to respond to natural and anthropogenic stressors. In marine systems, determining the scale, rate, and directionality of larval dispersal is therefore, central to understanding how coral metapopulations are interconnected and the degree of resiliency in the event of a localized d...
Article
Full-text available
We consider the opportunities and challenges associated with organizing a conference online, using a case study of a medium-sized (approx. 400 participants) international conference held virtually in August 2020. In addition, we present quantifiable evidence of the participants' experience using the results from an online post-conference questionna...
Preprint
Full-text available
Fine-scale larval dispersal and connectivity processes are key to species survival, growth, recovery and adaptation under rapidly changing disturbances. Quantifying both are required to develop any effective management strategy. In the present work, we examine the dispersal pattern and potential connectivity of a common deep-water coral, Paramurice...
Preprint
Full-text available
The degree of connectivity among populations influences their ability to respond to natural and anthropogenic stressors. In marine systems, determining the scale, rate, and directionality of larval dispersal is therefore central to understanding how coral metapopulations are interconnected and the degree of resiliency in the event of a localized di...
Preprint
Full-text available
Salting-out protocol for extracting high-molecular weight (HMW) genomic DNA from frozen octocorals for genomic methods. Suitable for genome sequencing, RAD-seq and other methods that require HMW DNA. Starting material must be alive when flash-frozen in liquid nitrogen and always stored below -80C.
Article
Full-text available
Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there i...
Article
Full-text available
Resource extraction from the ocean comes with ecosystem-wide risks, including threats to its biota such as the habitat forming corals that support elevated biomass and biodiversity. Despite catastrophic incidents like the Deepwater Horizon oil spill (DWHOS) disaster that occurred in 2010, offshore oil and gas drilling continues to occur around the...
Article
Full-text available
Mesophotic coral ecosystems (MCEs) are recognized around the world as diverse and ecologically important habitats. In the northern Gulf of Mexico (GoMx), MCEs are rocky reefs with abundant black corals and octocorals, including the species Swiftia exserta. Surveys following the Deepwater Horizon (DWH) oil spill in 2010 revealed significant injury t...
Article
Cold-seep chemosynthetic communities are found in patchy areas where methane and other hydrocarbons leak through the seafloor. Although relatively common in continental margins, chemosynthetic communities in the Caribbean region are poorly known. Their xistence in Colombian waters has been suggested by the presence of carbonates and specimens of se...
Article
The Cook-Austral volcanic lineament extends from Macdonald Seamount (east) to Aitutaki Island (west) in the South Pacific Ocean and consists of hotspot-related volcanic islands, seamounts, and atolls. The Cook-Austral volcanic lineament has been characterized as multiple overlapping, age-progressive hotspot tracks generated by at least two mantle p...
Article
Full-text available
Corals are some of the conspicuous taxa in deep-sea ecosystems. Yet, characterizing coral diversity is difficult and requires a combination of both morphological and genetic data. Many leading coral taxonomy experts are close-to retirement or have already retired. It is now imperative that the hands-on expertise that these taxonomists have – much o...
Article
Full-text available
Cold‐water corals (CWCs) are important foundation species in the world’s largest ecosystem, the deep sea. They support a rich faunal diversity but are threatened by climate change and increased ocean acidification. As part of this study, fragments from three genetically distinct Lophelia pertusa colonies were subjected to ambient pH (pH = 7.9) and...
Chapter
Full-text available
Annelids are invertebrates including polychaetes, earthworms and leeches, among others (Rouse & Pleijel 2001). Their body is segmented with numerous rings; locomotion is based on body perisltaltic movements aided by muscles and the coelom. Most annelids have bristles or chaetae with different levels of development and function. Reproduction may be...
Article
Full-text available
Background Attention to the deep-sea environment has increased dramatically in the last decade due to the rising interest in natural resource exploitation. Although Colombia holds a large submerged territory, knowledge of the seabed and its biodiversity beyond 1,000 m depth is very limited. During 2015–2017, Anadarko Colombia Company (ACC) carried...
Article
Full-text available
Range expansions driven by global change and species invasions may have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasi...
Article
Full-text available
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex disease of unknown etiology. Multiple studies point to disruptions in immune functioning in ME/CFS patients as well as specific genetic polymorphisms and alterations of the DNA methylome in lymphocytes. However, potential interactions between DNA methylation and genetic backgr...
Article
Full-text available
Deep‐sea coral communities are key components of the Gulf of Mexico ecosystem and were adversely affected by the Deepwater Horizon (DWH) oil spill. Coral colonies exposed to oil and dispersant exhibited mortality, damage, and physiological signatures of stress. Understanding how corals respond to oil and dispersant exposure at the molecular level i...
Preprint
Full-text available
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is an example of a complex disease of unknown etiology. Multiple studies point to disruptions in immune functioning in ME/CFS patients as well as with specific genetic polymorphisms and alterations of the DNA methylome in lymphocytes. However, the association between DNA methylation and ge...
Preprint
Full-text available
Range expansions driven by global change and species invasions are likely to have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point...
Article
Full-text available
Originally known as fossils from the Cambrian to the Devonian, the finding of a living monoplacophoran mollusc in 1952 was one of the great zoological discoveries of the twentieth century. Now, over 35 living species have been documented from deep-sea locations around the world, mainly from samples collected with trawls. Encountering these animals...
Article
Full-text available
Species inhabiting deep-sea hydrothermal vents are strongly influenced by the geological setting, as it provides the chemical-rich fluids supporting the food web, creates the patchwork of seafloor habitat, and generates catastrophic disturbances that can eradicate entire communities. The patches of vent habitat host a network of communities (a meta...
Article
Full-text available
Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequence...
Preprint
Full-text available
Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ∼7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequence...
Article
Full-text available
Background Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating idiopathic disease characterized by unexplained fatigue that fails to resolve with sufficient rest. Diagnosis is based on a list of symptoms and exclusion of other fatigue-related health conditions. Despite a heterogeneous patient population, immune and hypotha...
Article
Full-text available
The industrialization of the deep sea is expanding worldwide. Increasing oil and gas exploration activities in the absence of sufficient baseline data in deep-sea ecosystems has made environmental management challenging. Here, we review the types of activities that are associated with global offshore oil and gas development in water depths over 200...
Article
Species delimitations is problematic in many cases due to the difficulty of evaluating predictions from species hypotheses. In many cases delimitations rely on subjective interpretations of morphological and/or DNA data. Species with inadequate genetic resources needed to answer questions regarding evolutionary relatedness and genetic uniqueness ar...
Article
Full-text available
High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes - generically known as restriction-site associated DNA sequencing (RAD-seq) - is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is knowledge of the...
Article
Full-text available
PAR-CLIP, a CLIP-seq protocol, derives a transcriptome wide set of binding sites for RNA-binding proteins. Even though the protocol uses stringent washing to remove experimental noise, some of it remains. A recent study measured three sets of non-specific RNA backgrounds which are present in several PAR-CLIP datasets. However, a tool to identify th...
Preprint
Full-text available
High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes ? generically known as restriction-site associated DNA sequencing (RAD-seq) ? is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is a knowledge of th...
Preprint
Full-text available
Species delimitation is problematic in many taxa due to the difficulty of evaluating predictions from species delimitation hypotheses, which chiefly relay on subjective interpretations of morphological observations and/or DNA sequence data. This problem is exacerbated in recalcitrant taxa for which genetic resources are scarce and inadequate to res...
Data
Table S5 Results from Xia saturation test for each Sanger‐based genetic marker.
Data
Table S2 Accession numbers for sequences from the superorder Thoracica retrieved from GenBank.
Data
Table S8 Uncorrected pairwise genetic coxI distances (%) among specimens from Clade A
Data
Table S1 Collection and sequence information for the specimens used in this study.
Data
Table S3 Predictions of number of RAD‐tags in thoracician barnacles using SbfI. Data for Daphnia pulex obtained from the U.S. National Center for Biotechnology Information (NCBI) WGS database. Observed frequency of recognition sequences and calculated probability based on a trinucleotide genome composition model were generated following the methodo...
Data
Table S4 Nucleotide substitution models for each Sanger‐based genetic marker, as selected by the BIC criterion in jModeltest.
Data
Table S6 RAD sequencing results and filtering statistics.
Article
Full-text available
The characterization of evolutionary and biogeographical patterns is of fundamental importance to identify factors driving biodiversity. Due to their widespread but discontinuous distribution, deep-sea hydrothermal vent barnacles represent an excellent model for testing biogeographic hypotheses regarding the origin, dispersal, and diversity of mode...
Article
Full-text available
Characterization of large numbers of single nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions under selection in natural populations. To this end, population genomic approaches that harness the power of next-generation sequencing to underst...
Article
Full-text available
Numerous deep-sea species have apparent widespread and discontinuous distributions. Many of these are important foundation species, structuring hard-bottom benthic ecosystems. Theoretically, differences in the genetic composition of their populations vary geographically and with depth. Previous studies have examined the genetic diversity of some of...
Article
GALREX 2011 was a NOAA OER telepresence cruise that explored the diverse habitats and geologic settings of the deep Galápagos region. The expedition made12 Little Hercules ROV dives in July 2011.Abundant corals and a strong depth zonation of species (including deepwater coral communities) were found near 500 m depth on Paramount Seamount, likely in...
Article
From June to August 2010, an international partnership of scientists and engineers from the United States, Canada, and Indonesia utilized the NOAA Ship Okeanos Explorer and HD video from the ROV Little Herc to explore virtually unknown deep seafloor in the heart of the Coral Triangle. The INDEX-SATAL 2010 expedition bathymetrically mapped more than...
Article
The benthic ecosystems found in the deep-sea promontories of Sangihe Talaud region were explored, between June and August 2010, using the ROV Little Hercules aboard the NOAA ship Okeanos Explorer. The Sangihe-Talaud region is part of the Coral Triangle (CT) an area known for harboring the most biodiverse shallow-water coral reefs in the world. Notw...
Article
The INDEX-SATAL 2010 expedition began an international exploration of the seafloor in Indonesian waters using the methodology of telepresence, conducting EM302 multibeam mapping, water column CTD, and ROV high-definition video operations and sending data back to Exploration Command Centers in Indonesia and Seattle. Science observers in other locati...
Article
Full-text available
Este trabajo presenta datos sobre un brote de la Enfermedad de Plaga Blanca (EPB) en el banco de Serrana y resume siete años de observaciones de esta enfermedad en la vecina isla de San Andrés (Caribe colombiano). La mortalidad masiva de corales por causa de EPB se observó en la laguna del atolón (14° 27’ 53.24”, 80° 14’ 22.27” W, y 12m de profundi...