Jonathan B Geller

Moss Landing Marine Labs | MLML

Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workf...

DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxo...

Within the southern California Current ecosystem there are two well-documented breaks in marine community structure at Point Conception and Punta Eugenia. We explored the presence of similar breaks in a diverse zooplankton community through metabarcoding of mixed net tow tissue samples collected during an expedition from Monterey to Baja California...

With the increasing use of metagenetics for invasive species monitoring in aquatic habitats, fully assessing sample pre-processing is essential for appropriate data interpretation. This includes the impact of subsampling before DNA extraction, a common practice for processing zooplankton and other mixed samples where the volume of the sample exceed...

The Cytochrome C Oxidase subunit I gene (“COI”) is the de facto standard for animal DNA barcoding. Organism identification based on COI requires an accurate and extensive annotated database of COI sequences. Such a database can also be of value in reconstructing evolutionary history and in diversity studies. Two COI databases are currently availabl...

We announce the nearly complete mitochondrial genome sequences of two hexactinellid sponges, Bathydorus laniger and Docosaccus maculatus . A contiguous region of over 15,000 bp was sequenced from each genome. An uncommon structural element was identified as a series of repetitive elements with sequences matching cob in the genome of D. maculatus .

Twelve species of sponges (Calcarea and Demospongiae) were found on Japanese Tsunami Marine Debris (JTMD) that washed ashore in Oregon, Washington, and Hawai‘i. All taxa but one determined to species level are amphi-Pacific, with three having type localities in California (Leucosolenia eleanor Urban, 1906, Hymeniacidon sinapium de Laubenfels, 1930,...

A new species of the cheilostome bryozoan genus Bugula Oken, 1815, Bugula tsunamiensis, is described from Japan, having rafted across the North Pacific Ocean on numerous objects released into the ocean by the 2011 Great East Japan Earthquake and Tsunami, and landing in the Hawaiian Islands and on the Pacific Coast of the United States. This is the...

Twenty-eight species of hydroids are now known from Japanese tsunami marine debris (JTMD) sent to sea in March 2011 from the Island of Honshu and landing between 2012 and 2016 in North America and Hawai‘i. To 12 JTMD hydroid species previously reported, we add an additional 16 species. Fourteen species (50%) were detected only once; given the small...

In this study we used decades-old shells of the endangered Northeast Pacific white abalone Haliotis sorenseni to produce high-quality DNA sequences for identification and historical diversity analysis. We obtained mitochondrial (mt) and nuclear DNA sequences (cytochrome c oxidase subunit I and histone H3 respectively) from shells with collection da...

Biofouled debris from the 2011 Great East Japan earthquake and tsunami has landed in the Northeast Pacific and along the Hawaiian Islands since 2012. As of 2017, >630 biofouled debris items with >320 living species of algae, invertebrates, and fish have been examined. The invasive mussel Mytilus galloprovincialis was present on >50% of those items....

Long-distance life rafting When coastal ecosystems are affected by storms or tsunamis, organisms can be rafted across oceans on floating debris. However, such events are rarely observed, still less quantified. Carlton et al. chart the rafting journeys of coastal marine organisms across the Pacific Ocean after the 2011 East Japan earthquake and tsun...

The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to anal...

Detailed methodologies. (PDF)

PERMANOVA and ANOSIMs for motile preservation experiment OTU data (Table A and C, respectively), and data merged by phylum (Table B and D, respectively). (PDF)

One-Way ANOSIMs and Tukey tests showing differences in community composition retrieved by processing method (Table A) and preservation method (Table B). (PDF)

Accuracy of relaxed parameters (≥85% sequence similarity) when assigning to higher-level taxonomic ranks with Blastn. Data shown represent phyla distribution among queries. (PDF)

Raw data (top tables) and overall summary (bottom table) of the quantity of DNA and the percentage of that DNA that is > 1000 bp (as determined by ImageJ analysis) recovered from DNA extractions of sessile and motile ARMS samples across different processing and preservation methods. Bold values indicate low DNA quantity (<100 ng/ul) or quality (<20...

ANOSIMs and Tukey Tests for sessile processing experiment, data merged by phylum. ANOSIMs were carried out across all data for ARMS, processing method and preservation method. Tukey tests reported were calculated from all abundance data (* p ≤ 0.005, ** p ≤ 0.05, *** p > 0.05). (PDF)

One-Way ANOSIMs and Tukey Tests showing differences in community composition retrieved by processing method (OTU data; Table A), preservation method (OTU data; Table B) and differences in community richness retrieved by preservation and preservation method (OTU data; Table C). (PDF)

One-Way ANOSIMs and Tukey tests showing differences in community composition retrieved by processing and preservation method, void of Rhodophyta, for OTU data (Table A) and data merged by phylum (Table B). (PDF)

ANOSIMs and Tukey Tests for sessile processing experiment (OTU data). ANOSIMs were carried out across all data for ARMS, processing method and preservation method. Tukey tests reported were calculated from all abundance data (* p ≤ 0.005, ** p ≤ 0.05, *** p > 0.05). (PDF)

SIMPER analysis of the subset of the communities retrieved from the sessile processing experiment, used in comparison with CPCe (Coral Point Count) data. Tables show phylum level differences in community composition between SIMPROF clusters, which compared community composition data retrieved from different processing methods and CPCe image analysi...

SIMPER analysis showing phylum level differences in community composition across all data from the sessile processing experiment, as retrieved by processing method (Table A; top table) and preservation technique (Table A; bottom table) and partitioned by preservation method (Table B; top two tables) and processing method (Table B; bottom two tables...

Conflicting and altered taxonomies in database searches. (PDF)

PERMANOVA for sessile processing experiment (OTU data). (PDF)

Phylum level identifications of OTUs and their relative abundance by ARMS fraction. Bold text represents most abundant phyla in each fraction. (PDF)

Diversity data for sessile processing experiment, showing number of OTUs (S), species richness (Margalef; d), Pielou's eveness (J'), and Shannon diversity (H'). Based on rarefied abundance data, void of singletons. (PDF)

PERMANOVA for sessile processing experiment, data merged by phylum. (PDF)

The movement of biofouling organisms by ships results in the transfer of marine species across biogeographical boundaries on a global scale. We used barnacles, a relatively well-studied taxon, to investigate the extent to which modern commercial vessels disperse biofouling species beyond their current known ranges. Vessels predominantly operated in...

Anthropogenic vectors have moved marine species around the world leading to increased invasions and expanded species' ranges. The biotic resistance hypothesis of Elton (in The ecology of invasions by animals and plants, 1958) predicts that more diverse communities should have greater resistance to invasions, but experiments have been equivocal. We...

Reduced genetic diversity due to founder effects often is expected for invasive populations. The present study examined two nuclear gene regions and one mitochondrial gene to evaluate the origins and genetic diversity of Gemma gemma, a ‘stow-away’ that was introduced to California more than 100 years ago with the importation of the Eastern oyster,...

Fourteen species of hydroids, including two anthoathecates and 12 leptothecates, are reported from the west coast of North America on debris from the tsunami that struck Japan on 11 March 2011. Six species were found on a dock that stranded at Agate Beach, Newport, Oregon, five from a boat at Gleneden Beach, Oregon, four from a dock in Olympic Nati...

Corallimorpharia is a small Order of skeleton-less animals that is closely related to the reef-building corals (Scleractinia) and of fundamental interest in the context of understanding the potential impacts of climate change in the future on coral reefs. The relationship between the nominal Orders Corallimorpharia and Scleractinia is controversial...

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of g...

Our understanding of reef corals and their fate in a changing climate is limited by our ability to monitor the diversity and abundance of the dinoflagellate endosymbionts that sustain them. This study combined two well-known methods in tandem: fluorescent in situ hybridization (FISH) for genotype-specific labeling of Symbiodinium and flow cytometry...

DNA barcoding is a powerful tool for species detection, identification and discovery. Metazoan DNA barcoding is primarily based upon a specific region of the cytochrome c oxidase subunit I gene that is PCR amplified by primers HCO2198 and LCO1490 ('Folmer primers') designed by Folmer et al. (Molecular Marine Biology and Biotechnology, 3, 1994, 294)...

Two new species of glass sponge were discovered from the abyssal plain 200 km west of the coast of California (Station M). The sponges have similar gross morphology—an unusual plate-like form with basalia stilting the body above soft abyssal sediments. Bathydorus laniger sp. n. differs from its congeners by the presence of dermal and atrial staurac...

We evaluated mercury (Hg) exposure and two biomarkers, metallothionein (MT) gene expression and histopathological alterations in a wild fish species, largemouth bass (Micropterus salmoides), collected from the Sacramento-San Joaquin Delta, CA, a region polluted with Hg from historic mining activities. Hg is highly toxic and can disrupt multiple phy...

Watersipora is an invasive genus of bryozoans, easily dispersed by fouled vessels. We examined Cytochrome c oxidase subunit I haplotypes from introduced populations on the US Pacific coastline to investigate geographic segregation of species and/or haplotypes. In California, the W. subtorquata group fell into three major sub-groups: W. subtorquata...

ABSTRACT: A non-native bryozoan, Schizoporella errata, forms extensive patches of free-living balls and reef-like structures (bryoliths) on the mudflats in south San Francisco Bay, California. The ball-like bryoliths range from 2 to 20 cm in diameter, and the reef-like structures can be nearly 1 m across. While S. errata is known to form bryoliths...

The brine shrimp Artemia franciscana was used as a model zooplankter to explore the range and accuracy of quantitative PCR (QPCR) in detecting a target species in plankton community DNA. Specific primers were designed in the 18S ribosomal RNA and mitochondrial cytochrome c oxidase subunit I genes and analyzed by TaqMan and SYBR Green I reporting sy...

Aim Historical information about source populations of invasive species is often limited; therefore, genetic analyses are used. We compared inference about source populations from historical and genetic data for the oyster-associated clam, Gemma gemma that invaded California from the USA Atlantic coast. Location Mid-Atlantic (North Carolina, Maryla...

Aim Historical information about source populations of invasive species is often limited; therefore, genetic analyses are used. We compared inference about source populations from historical and genetic data for the oyster-associated clam, Gemma gemma that invaded California from the USA Atlantic coast. Location Mid-Atlantic (North Carolina, Maryla...

The extent to which the geographic distributions of marine organisms have been reshaped by human activities remains underappreciated, and so does, consequently, the impact of invasive species on marine ecosystems. The application of molecular genetic data in fields such as population genetics, phylogeography, and evolutionary biology have improved...

Aim The European green crab (Carcinus maenas) expanded dramatically after its introduction to the west coast of North America, spreading over 1000 km in < 10 years. We use samples of Carcinus maenas collected over time and space to investigate the genetic patterns underlying the species’ initial establishment and spread, and discuss our findings in...

Seamounts are unique and biologically productive deep-sea habitats that have often been described as having high levels of endemism, highly productive fisheries, and benthic communities vulnerable to trawl fishing. We describe the abundance and distribution of benthic megafaunal invertebrates found on 3 seamounts off central and southern California...

A large number of glass shrimp, Pasiphaea pacifica Rathburn 1902, were collected in a Tucker trawl aboard the R/V Point Sur in Monterey Bay, California during November 2006. Upon inspection, the shrimp were found to be harboring several symbionts, including a hydroid colony (Cnidaria: Hydrozoa) of unknown affinity. Shrimp-bearing hydroids were retu...

The European green crab Carcinus maenas is one of the world's most successful aquatic invaders, having established populations on every continent with temperate shores. Here we describe patterns of genetic diversity across both the native and introduced ranges of C. maenas and its sister species, C. aestuarii, including all known non-native populat...