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Reads were grouped into OTUs using the following swarm-based pipeline: paired-end reads were merged with vsearch’s --fastq_mergepairs command (version 2.15.1, allowing for staggered reads; Rognes et al., 2016), and trimmed with cutadapt (version 3.0; Martin, 2011), keeping only reads containing both forward and reverse primers. After trimming, the expected error per read was estimated with vsearch’s command --fastq_filter and the option --eeout. Each sample was then de-replicated, i.e. strictly identical reads were merged, using vsearch’s command --derep_fulllength, and converted into fasta format. Clustering was performed at the sample level with swarm 3.0 using default parameters (Mahé et al., 2015). Prior to global clustering, individual fasta files (one per sample) were pooled and further dereplicated with vsearch. Files containing per-read expected error values were also dereplicated to retain only the lowest expected error for each unique sequence. Global clustering was performed with swarm (using the fastidious option). Cluster representative sequences were then searched for chimeras with vsearch’s command --uchime_denovo using default parameters (Edgar et al., 2011). Clustering results, expected error values, taxonomic assignments, and chimera detection results were used to build a “raw” occurrence table. Reads without primers, reads shorter than 32 nucleotides and reads with uncalled bases (“N”) were discarded. For a “filtered” occurrence table, non-chimeric sequences, sequences with an expected error per nucleotide below 0.0002, and clusters containing at least 2 reads were retained. Since primer trimming is not perfect, some sequences can still contain primer fragments or be excessively trimmed. These sub- or super-sequences were identified using vsearch and merged with their closest, most abundant perfectly trimmed sequence. Finally, occurrence patterns throughout our sample collection were used to further refine the occurrence table. Clusters that contain sub-clusters with only a single-nucleotide difference but with different ecological patterns (defined here as uncorrelated abundance values in at least 5% of the samples) were turned into distinct clusters (https://github.com/frederic-mahe/fred-metabarcoding-pipeline). On the other hand, clusters with similar sequences that had correlated abundance values in at least 95% of the samples, were merged using a re-implementation of lulu's method (Frøslev et al. 2017; https://github.com/frederic-mahe/mumu).

Time and energy are finite resources in any environment, and how and when organisms use their available resources to survive and reproduce is the crux of life history theory (Gadgil and Bossert 1970; Balon 1975; Stearns 1976). The different survival strategies used by animals are often shaped by their environment in addition to their biology (Winemiller and Rose 1992), which allows for exploration into biological variability when environmental factors are known. For this reason, the Line Islands in the Central Pacific provide an ideal location to perform observational studies due to their unique productivity gradient and fish assemblage structures across the island chain (Sandin et al. 2008; DeMartini et al. 2008; Fox et al. 2018; Zgliczynski et al. 2019). Many of the world’s coral reefs are in remote regions that lack monitoring programs or even local populations, so conducting ecological surveys on fish communities in these regions can require extensive amounts of time, energy, resources and people. The inherent variability an environment exerts on the many factors that contribute to growth over a lifetime make it difficult to generate a directly proportional formula that calculates age. A novel age estimation method was developed that utilizes in-situ visual census data to estimate the age of fishes, and as a case study, several fish were chosen as representative species to explore its capabilities. Through this process, new ecological information and insight can be gained about the age structures of fish populations both between and throughout the Line Islands.

Understanding fish diversity patterns is critical for fisheries management amidst overfishing and climate change. Fish egg surveys have been used to characterize pelagic spawning fish communities, estimate biomass, and track population trends in response to perturbations. Environmental DNA (eDNA) metabarcoding has been implemented to rapidly and non-invasively survey marine ecosystems. To understand the efficacy of eDNA metabarcoding for assessing pelagic spawning fish community composition, concurrent eDNA metabarcoding and fish egg DNA barcoding off Scripps Institution of Oceanography’s Pier (La Jolla, CA) were conducted. Both methods revealed seasonal patterns in agreement with previous fish and fish egg surveys. Species richness was highest in late spring and summer. The presence and spawning of commercially important species and species of conservation concern were detected. Both methods showed overlap for pelagic spawning fishes for broadcast spawners, schooling fish, and locally abundant species. Some actively spawning species were not co-detected with eDNA, likely due to different sampling strategies, taxonomic biases, and abiotic/biotic factors influencing eDNA transport, shedding, and degradation. We identified key advantages and disadvantages of each method. Fish egg barcoding provided information on spawning trends but did not detect taxa with alternate reproduction strategies. Metabarcoding eDNA detected species not found in fish egg sampling, including demersal and viviparous bony fishes, non-spawning adults, Chondrichthyan, and Mammalian species, but missed abundant pelagic fish eggs. This study demonstrates that DNA barcoding of fish eggs and eDNA metabarcoding work best in tandem as each method identified unique fish taxa and provided complementary ecological and biological insight.

The western North Atlantic is a dynamic region characterized by the Gulf Stream western boundary current and inhabited by a diverse host of odontocete, or toothed whale, top predators. Their habitats are highly exploited by commercial fisheries, shipping, marine energy extraction, and naval exercises, subjecting them to a variety of potentially harmful interactions. Many of these species remain poorly understood due to the difficulties of observing them in the pelagic environment. Their habitat utilization and the impacts of anthropogenic activities are not well known. Over the past decade, passive acoustic data has become increasingly utilized for the study of a wide variety of marine animals, and offers several advantages over traditional line-transect visual survey methods. Passive acoustic devices can be deployed at offshore monitoring sites for long periods of time, enabling detection of even rare and cryptic species across seasons and sea states, and without altering animal behaviors. Here we utilized a large passive acoustic data set collected across a latitudinal habitat gradient in the western North Atlantic to address fundamental knowledge gaps in odontocete ecology. I approached the problem of discriminating between species based on spectral and temporal features of echolocation clicks by using machine learning to identify novel click types, and then matching these click types to species using spatiotemporal correlates. I was able to identify novel click types associated with short-beaked common dolphins, Risso’s dolphins, and short-finned pilot whales in this way. Next I characterized temporal patterns in presence and activity for ten different species across our monitoring sites at three different temporal scales: seasonal, lunar, and diel. I observed spatiotemporal separation of apparent competitors, and complex behavioral patterns modulated by interactions between the seasonal, lunar, and diel cycles. Finally I investigated the relationships between species presence and oceanographic covariates to predict habitat suitability across the region, and explored niche partitioning between potentially competitive species. The insights gained here significantly advance our understanding of toothed whale ecology in this region, and can be used for more effective population assessments and management in the face of anthropogenic threats and climate change.

Permafrost is warming globally which leads to widespread permafrost thaw. Particularly ice-rich permafrost is vulnerable to rapid thaw and erosion, impacting whole landscapes and ecosystems. Abrupt permafrost disturbances, such as retrogressive thaw slumps (RTS), expand by several meters each year and lead to an increased soil organic carbon release. We applied the disturbance detection algorithm LandTrendr for automated large-scale RTS mapping and high temporal thaw dynamic assessment to Northeast Siberia (8.1 × 10^6km^2). We adapted and parametrised the temporal segmentation algorithm for abrupt disturbance detection to incorporate Landsat+Sentinel-2 mosaics, conducted spectral filtering, spatial masking and filtering, and a binary machine-learning object classification of the disturbance output to separate between RTS and false positives (F1 score: 0.61). Ground truth data for calibration and validation of the workflow was collected from 9 known RTS cluster sites using very high-resolution RapidEye and PlanetScope imagery. The data set presents the results of the first automated detection and assessment of RTS and their temporal dynamics at large-scale for 2001–2019. We identified 50,895 RTS and a steady increase in RTS-affected area from 2001 to 2019 across Northeast Siberia, with a more abrupt increase from 2016 onward. Overall the RTS-affected area increased by 331% compared to 2000 (2000: 20,158 ha, 2001-2019: 66,699 ha). Contrary to this, focus sites show spatio-temporal variability in their annual RTS dynamics, with alternating periods of increased and decreased RTS development, indicating a close relationship to thaw drivers. The detected increase in RTS dynamics suggests advancing permafrost thaw and underlines the importance of assessing abrupt permafrost disturbances with high spatial and temporal resolution at large-scales. This consistenly obtained disturbance product will help to parametrise regional and global climate change models.

Coccolithophorid algae are microscopic but prolific calcifiers in modern and ancient oceans. When the pH of seawater is modified, as may occur in the future due to ocean acidification, different species and strains of coccolithophorids have exhibited diverse calcification responses in laboratory culture. Since their biomineralization is a completely intracellular process, it is unclear why their response should be affected by extracellular seawater pH. Variations in the B/Cain coccoliths are potential indicators of pH shifts in the intracellular coccolith vesicle where calcification occurs, because B/Ca in abiogenic calcites increases at higher pH due to the greater abundance of borate ions, the only B species incorporated into calcite. We used a SIMS ion probe to measure B/Ca of coccoliths from three different strains of Emiliania huxleyi and one strain of Coccolithus braarudiibraarudiicultured under different seawater pH conditions to ascertain if the B/Ca can be used to elucidate how coccolithophorids respond to changing ocean pH.These data are interpreted with the aid of a conceptual model of cellular boron acquisition by coccolithophorids. Based on uptake in other plants, we infer that boron uptake by coccolithophorid cells is dominated by passive uptake of boric acid across the lipid bilayer. Subsequently, in the alkaline coccolith vesicle (C.V.), boron speciates according to the C.V. pH, and borate is incorporated into the coccolith. At increasing seawater pH, the relative abundance of the neutral boric acid in seawater decreases, lowering the potential B flux into the cell. Homeostasis or constant pH of the coccolith vesicle results in a decrease of the B/Cain the coccolith with increasing seawater pH. In contrast, if coccolith vesicle pH increases with increasing seawater pH, then the B/Ca will increase as the fraction of borate in the coccolith vesicle increases. The coccolith B/Ca is also expected to depend inversely on the dissolved inorganic carbon (DIC) concentration in the coccolith vesicle. The B/Ca in cultured coccoliths is much lower than that of foraminifera or corals and limits precision in the analysis. Modest variations in DIC or pH of the coccolith vesicle can account for the observed trends in B/Ca in cultured coccoliths. The model shows that paired measurements of B/Ca and B isotopic composition of the calcite could distinguish between regulation of pH or DIC in the coccolith vesicle. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2022-10-21.

The total snow and ice thickness (distance from the snow surface to the ice-ocean interface) was measured by the electromagnetic induction (EM) method. On MOSAiC transects, we used a broad-band EM instrument sensor (GEM-2 by Geophex Ltd) towed on a small sled (Hunkeler et al, 2015; Hunkeler et al, 2016). The instrument includes a real-time data processing unit including a GPS receiver which communicates with a pocket PC that is operates the sensor and records the EM and GPS data streams. The GEM-2 is a broadband sensor that can transmit multiple configurable frequencies in the kHz range simultaneously. The sensor setup during MOSAiC used 5 frequencies with an approximately logarithmic spacing throughout the frequency range of the sensor (1.525 kHz, 5.325 kHz, 18.325 kHz, 63.025 kHz, and 93.075 kHz). The transect measurements are based on an empirical approach based on a sensor calibration, where the GEM-2 was placed at known heights above the sea ice surface using a wooden ladder on top of level ice with a known thickness determined by 5 drill holes. An exponential function was then fitted to the frequency components as function of distance of the sensor to the ice/ocean interface and then applied to the transect data. The closest-in-time calibration result was used when a GEM-2 survey could not be accompanied with a calibration. The total thickness retrieval with the GEM-2 calibration and survey data was done on-board shortly after each profile. The dataset is therefore labeled as GEM-2 quickview data but has been subject to manual quality control. Using a direct relationship between total thickness and frequency component implies the assumption that the sea ice conductivity is negligible and the ice/water interface constant within the GEM-2 footprint. While this is a reasonable assumption for level ice, the peak thicknesses of ridges are known to be underestimated by as much as 50 % (Pfaffing et al, 2007) and will be subject of further processing. To estimate the snow depth and then subtract its thickness from the total thickness we rely on direct measurements of snow depth with Magnaprobe. The co-inciding snow depth measurements on MOSAiC transect can be found here: https://doi.pangaea.de/10.1594/PANGAEA.937781 Not every GEM-2 transect has complimentary snow depth measurements. An overview of all transect measurements at MOSAiC is given in the attached table. For more details we refer to the MOSAiC transect paper by Itkin et al, 2022: Sea ice and snow mass balance from transects in the MOSAiC Central Observatory, in review at Elementa – Science of Anthropocene.

Amines were measured by aerosol mass spectrometry (AMS) and Fourier Transform Infrared (FTIR) spectroscopy during the North Atlantic Aerosols and Marine Ecosystems Study (NAAMES) cruises. Both AMS non-refractory (NR) amine ion fragments comprising the AMS CxHyNz family and FTIR non-volatile (NV) amine measured as primary (C-NH2) amine groups typically had greater concentrations in continental air masses than marine air masses. Secondary continental sources of AMS NR amine fragments were identified by consistent correlations to AMS NR nitrate, AMS NR m/z 44, IC non-sea salt potassium, and radon for most air masses. FTIR NV amine group mass concentrations for particles with diameters <1 μm showed large contributions from a primary marine source that was identified by significant correlations with measurements of wind speed, chlorophyll a, seawater dimethylsulfide (DMS), AMS NR chloride, and ion chromatography (IC) sea salt as well as FTIR NV alcohol groups in both marine and continental air masses. FTIR NV amine group mass concentrations in <0.18 μm and <0.5 μm particle samples in marine air masses likely have a biogenic secondary source associated with strong correlations to FTIR NV acid groups, which are not present for <1 μm particle samples. The average seasonal contribution of AMS NR amine fragments and FTIR NV amine groups ranged from 27% primary marine amine and 73% secondary continental amine during Early Spring to 53% primary amine and 47% secondary continental amine during Winter. These results demonstrate that AMS NR and FTIR NV amine measurements are complementary and can be used together to investigate the variety and sources of amines in the marine environment.

This project is directed towards implementing aspects of the tidewater goby recovery plan in coordination with, and funded by, the US Fish & Wildlife Service (USFWS) through a Section 6 Cooperative Agreement awarded to the University of California, Los Angeles on May 15, 2015. The primary focus of this dissertation was to developed a quantitative framework to complete a metapopulation viability analysis (MVA) for the endangered tidewater gobies in the genus Eucyclogobius. Modeling tidewater goby metapopulation dynamics is an essential component in constructing long-term management plans rangewide throughout the California Coast. This dissertation examines more closely how these dynamics affect viability, connectivity, and long-term persistence of tidewater goby metapopulations throughout the California coast. In the first chapter of this dissertation, I conducted annual population surveys (2014, 2015, and 2017-2018) in 117 estuaries and lagoons to assess the current health and status of the tidewater gobies in five of the six Recovery Units, spanning from Bodega Bay to San Diego, CA. This massive effort has provided continuous coastal surveys over four years, and over 300 observations, which helped create the framework for a robust and comprehensive presence/absence dataset to help inform metapopulation management and recovery actions. In the second chapter of this dissertation collated all existing rangewide occupancy data, metapopulation descriptors, wetland site characteristics, and repository specimen collections into an open access database. This database will provide critical information relative to the federally endangered tidewater gobies and help inform the metapopulation viability analysis model developed in this study, as well as support continued research on the conservation and management of these incredible fish species and the coastal wetland ecosystems they inhabit. In the third chapter of this dissertation I review the general biology, conservation status, habitat impacts, and metapopulation dynamics of the northern tidewater goby (Eucyclogobius newberryi) and southern tidewater goby (Eucyclogobius kristinae). In addition, I demonstrate the effectiveness of a Bayesian approach to provide a flexible method to generate metapopulation viability analyses and provide a detailed summary of the MVA model framework, including limitations, required corrections, and future amendments that need to be addressed in order to meet the recovery criterion envisioned in the recovery plan.

Parasites and pathogens exert strong selection on their hosts and alter the structure, diversity, and productivity of communities of ecosystems. This paper presents results of a survey of parasite composition and prevalence observed on and within the freshwater hybrids Owens (Siphateles bicolor snyderi) and Lahontan (Siphateles bicolor obesa) Tui Chubs, a native minnow species, in the Eastern Sierra Nevada mountains of California. The Owen and Lahontan Tui Chub is present in many lakes and rivers in Northern California and its parasite community has yet to be characterized. My thesis asks what kinds of parasites are found in the freshwater Tui Chub, which lakes or streams held the highest parasitic loads, and which features of individual fish and the habitat influence parasite density and/or types of parasites. Fish samples were collected in Summer 2019 by PhD student Henry Baker at 10 different sampling sites including freshwater lakes and streams that vary in size, temperature, water chemistry and species present across Owens Valley, California. I dissected 134 individual fish to characterize the ecto- and endo-parasite communities. My results show that two of the locations had significantly higher parasite infection rates than the others, where few macroscopic parasites were observed. These two locations were both geothermal with warmer waters and distinct water chemistry with high salinity and alkalinity. This pattern suggests that some aspects of geothermal habitat favor the parasite life cycle and makes fish in these sites more easily accessible as a host, though the mechanism behind the pattern is unknown. Four main types of visually distinct parasites were found: one adult life-stage tapeworm, one adult life- stage nematode and two metacercaria trematodes, though none were identified taxonomically. The greater parasite infection rates in geothermal habitats may be related to the greater abundance of snails in these sites, which may serve as intermediate hosts to fish parasites. No differences in parasite infection rates or composition were observed between lake and stream habitats. My thesis suggests that the atypical thermal and chemical environment of geothermal springs promotes parasitism in Tui Chub, but that lakes and streams are similar in containing low rates of infection by any parasites among fish.