College of Science
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Item 3D Genital shape complexity in female marine mammals(Wiley Online Library, 2021-02-15) Orbach, Dara N.; Brassey, Charlotte A.; Gardiner, James D.; Brennan, Patricia L. R.; Orbach, Dara N.; Brassey, Charlotte A.; Gardiner, James D.; Brennan, Patricia L. R.Comparisons of 3D shapes have recently been applied to diverse anatomical structures using landmarking techniques. However discerning evolutionary patterns can be challenging for structures lacking homologous landmarks. We used alpha shape analyses to quantify vaginal shape complexity in 40 marine mammal specimens including cetaceans, pinnipeds, and sirenians. We explored phylogenetic signal and the potential roles of natural and sexual selection on vaginal shape evolution. Complexity scores were consistent with qualitative observations. Cetaceans had a broad range of alpha complexities, while pinnipeds were comparatively simple and sirenians were complex. Intraspecific variation was found. Three-dimensional surface heat maps revealed that shape complexity was driven by invaginations and protrusions of the vaginal wall. Phylogenetic signal was weak and metrics of natural selection (relative neonate size) and sexual selection (relative testes size, sexual size dimorphism, and penis morphology) did not explain vaginal complexity patterns. Additional metrics, such as penile shape complexity, may yield interesting insights into marine mammal genital coevolution. We advocate for the use of alpha shapes to discern patterns of evolution that would otherwise not be possible in 3D anatomical structures lacking homologous landmarks.Item A 10-year Metocean dataset for Laguna Madre, Texas, including for the study of extreme cold events(2023-11-28) White, Miranda C.; Vicens-Miquel, Marina; Tissot, Philippe; Krell, EvanCoastal observations along the Texas coast are valuable for many stakeholders in diverse domains. However, the management of the collected data has been limited, creating gaps in hydrological and atmospheric datasets. Among these, water and air temperature measurements are particularly crucial for water temperature predictions, especially during freeze events. These events can pose a serious threat to endangered sea turtles and economically valuable fish, which can succumb to hypothermic stunning, making them vulnerable to cold-related illness or death. Reliable and complete water and air temperature measurements are needed to provide accurate predictions of when cold-stunning events occur. To address these concerns, the focus of this paper is to describe the method used to create a complete 10-year dataset that is representative of the upper Laguna Madre, TX using multiple stations and various gap-filling methods. The raw datasets consist of a decade’s worth of air and water temperature measurements within the Upper Laguna Madre from 2012 to 2022 extracted from the archives of the Texas Coastal Ocean Observation Network and the National Park Service. Large portions of data from the multiple stations were missing from the raw datasets, therefore a systematic gap-filling approach was designed and applied to create a near-continuous dataset. The proposed imputation method consists of three steps, starting with a short gap interpolation method, followed by a long gap-filling process using nearby stations, and finalized by a second short gap interpolation method. This systematic data imputation approach was evaluated by creating random artificial gaps within the original datasets, filling them using the proposed data imputation method, and assessing the viability of the proposed methods using various performance metrics. The evaluation results help to ensure the reliability of the newly imputed dataset and the effectiveness of the data imputation method. The newly created dataset is a valuable resource that transcends the local cold-stunning issue, offering viable utility for analyzing temporal variability of air and water temperatures, exploring temperature interdependencies, reducing forecasting uncertainties, and refining natural resource and weather advisory decision-making processes. The cleaned dataset with minimal gaps (<2%) is ready and convenient for artificial intelligence and machine learning applications.Item A meta-analysis of disturbance caused by drones on nesting birds(2023) Cantu de Leija, Antonio; Mirzadi, Rostam E.; Randall, Jessica M.; Portmann, Maxwell D.; Mueller, Erin J.; Gawlik, Dale E.The use of drones for monitoring nesting birds is rapidly increasing given their affordability and efficiency in bird detection and quantification across habitats. Reports of disturbance caused by drones on different bird species have been mixed, with no consensus on the degree to which different factors affect disturbance responses. Given the lack of systematic assessments of disturbance from drones on nesting birds, we conducted a formal meta-analysis to quantify the degree of disturbance caused by multi-rotor drones on nesting birds, with a particular focus on the effects of altitude of flights and species nesting traits. Seventeen studies met our criteria for inclusion in the analysis, from which we extracted 31 effect sizes in the form of log-odds ratio. Drones showed a small disturbance effect (-1.54; 95% CI: -2.83, -0.26) on nesting birds overall, but heterogeneity was large. Drone flights > 50 m showed no evidence of disturbance on nesting birds. Conversely, flights at lower altitudes (≤ 50 m) showed stronger evidence of disturbance effects, with the largest odds of disturbance observed on ground solitary and non-ground solitary nesters. Only ground colonial nesters showed no evidence of disturbance regardless of the drone altitude. We conclude that the use of drones can be an efficient and safe means of surveying nesting birds if altitude and nesting traits are considered in survey protocols. RESUMEN. El uso de drones para monitorear las aves que anidan está aumentando rápidamente dada su asequibilidad y eficiencia en la detección y cuantificación de aves en todos los hábitats. Los informes de perturbaciones causadas por drones en diferentes especies de aves han sido mixtos, sin consenso sobre el grado en que los diferentes factores afectan las respuestas de perturbación. Dada la falta de evaluaciones sistemáticas de la perturbación de los drones en las aves que anidan, realizamos un metanálisis formal para cuantificar el grado de perturbación causada por drones multirotor en las aves que anidan, haciendo foco en particular en los efectos de la altitud de los vuelos y los rasgos de anidación de las especies. Diecisiete estudios cumplieron los criterios de inclusión en el análisis, de los cuales se extrajeron 31 tamaños del efecto en forma de relación logarítmica de probabilidades. Los drones mostraron un pequeño efecto de perturbación (-1,54; IC del 95%: -2,83, -0,26) en las aves que anidan en general, pero la heterogeneidad fue grande. Los vuelos de drones > 50 m no mostraron evidencia de perturbación en las aves que anidan. Por el contrario, los vuelos a altitudes más bajas (≤ 50m) mostraron una mayor evidencia de efectos de perturbación, con las mayores probabilidades de perturbación observadas en anidadores solitarios y no terrestres. Solo los anidadores coloniales terrestres no mostraron evidencia de perturbación, independientemente de la altitud del dron. Concluimos que el uso de drones puede ser un medio eficiente y seguro para inspeccionar las aves que anidan si la altitud y los rasgos de anidación se consideran en los protocolos de monitoreo.Item Abundance, size, and survival of recruits of the reef coral Pocillopora acuta under ocean warming and acidification(2020-02-04) Bahr, Keisha D.; Tran, Tiana; Jury, Christopher P.; Toonen, Robert J.Ocean warming and acidification are among the greatest threats to coral reefs. Massive coral bleaching events are becoming increasingly common and are predicted to be more severe and frequent in the near future, putting corals reefs in danger of ecological collapse. This study quantified the abundance, size, and survival of the coral Pocillopora acuta under future projections of ocean warming and acidification. Flow-through mesocosms were exposed to current and future projections of ocean warming and acidification in a factorial design for 22 months. Neither ocean warming or acidification, nor their combination, influenced the size or abundance of P. acuta recruits, but heating impacted subsequent health and survival of the recruits. During annual maximum temperatures, coral recruits in heated tanks experienced higher levels of bleaching and subsequent mortality. Results of this study indicate that P. acuta is able to recruit under projected levels of ocean warming and acidification but are susceptible to bleaching and mortality during the warmest months.Item Abundance, size, and survival of recruits of the reef coral Pocillopora acuta under ocean warming and acidification(PLOS ONE, 2020-02-04) Tran, Tiana; Jury, Christopher P.; Bahr, Keisha D.; Toonen, Robert J.Ocean warming and acidification are among the greatest threats to coral reefs. Massive coral bleaching events are becoming increasingly common and are predicted to be more severe and frequent in the near future, putting corals reefs in danger of ecological collapse. This study quantified the abundance, size, and survival of the coral Pocillopora acuta under future projections of ocean warming and acidification. Flow-through mesocosms were exposed to current and future projections of ocean warming and acidification in a factorial design for 22 months. Neither ocean warming or acidification, nor their combination, influenced the size or abundance of P. acuta recruits, but heating impacted subsequent health and survival of the recruits. During annual maximum temperatures, coral recruits in heated tanks experienced higher levels of bleaching and subsequent mortality. Results of this study indicate that P. acuta is able to recruit under projected levels of ocean warming and acidification but are susceptible to bleaching and mortality during the warmest months.Item Acclimatization drives differences in reef-building coral calcification rates(MDPI, 2020-09-08) Barnhill, Kelsey Archer; Jogee, Nadia; Brown, Colleen; McGowan, Ashley; Rodgers, Ku’ulei; Bryceson, Ian; Bahr, Keisha D.; Barnhill, Kelsey Archer; Jogee, Nadia; Brown, Colleen; McGowan, Ashley; Rodgers, Ku’ulei; Bryceson, Ian; Bahr, Keisha D.Coral reefs are susceptible to climate change, anthropogenic influence, and environmental stressors. However, corals in Kāneʻohe Bay, Hawaiʻi have repeatedly shown resilience and acclimatization to anthropogenically-induced rising temperatures and increased frequencies of bleaching events. Variations in coral and algae cover at two sites—just 600 m apart—at Malaukaʻa fringing reef suggest genetic or environmental differences in coral resilience between sites. A reciprocal transplant experiment was conducted to determine if calcification (linear extension and dry skeletal weight) for dominant reef-building species, Montipora capitata and Porites compressa, varied between the two sites and whether or not parent colony or environmental factors were responsible for the differences. Despite the two sites representing distinct environmental conditions with significant differences between temperature, salinity, and aragonite saturation, M. capitata growth rates remained the same between sites and treatments. However, dry skeletal weight increases in P. compressa were significantly different between sites, but not across treatments, with linear mixed effects model results suggesting heterogeneity driven by environmental differences between sites and the parent colonies. These results provide evidence of resilience and acclimatization for M. capitata and P. compressa. Variability of resilience may be driven by local adaptations at a small, reef-level scale for P. compressa in Kāneʻohe Bay.Item Acclimatory plasticity drives differences in reef-building coral calcification rates(MDPI, 2020-09-08) Barnhill, Kelsey Archer; Jogee, Nadia; Brown, Colleen; McGowan, Ashley; Rodgers, Ku’ulei; Bryceson, Ian; Bahr, Keisha D.; Barnhill, Kelsey Archer; Jogee, Nadia; Brown, Colleen; McGowan, Ashley; Rodgers, Ku’ulei; Bryceson, Ian; Bahr, Keisha D.Coral reefs are susceptible to climate change, anthropogenic influence, and environmental stressors. However, corals in Kāneʻohe Bay, Hawaiʻi have repeatedly shown resilience and acclimatization to anthropogenically-induced rising temperatures and increased frequencies of bleaching events. Variations in coral and algae cover at two sites—just 600 m apart—at Malaukaʻa fringing reef suggest genetic or environmental differences in coral resilience between sites. A reciprocal transplant experiment was conducted to determine if calcification (linear extension and dry skeletal weight) for dominant reef-building species, Montipora capitata and Porites compressa, varied between the two sites and whether or not parent colony or environmental factors were responsible for the differences. Despite the two sites representing distinct environmental conditions with significant differences between temperature, salinity, and aragonite saturation, M. capitata growth rates remained the same between sites and treatments. However, dry skeletal weight increases in P. compressa were significantly different between sites, but not across treatments, with linear mixed effects model results suggesting heterogeneity driven by environmental differences between sites and the parent colonies. These results provide evidence of resilience and acclimatization for M. capitata and P. compressa. Variability of resilience may be driven by local adaptations at a small, reef-level scale for P. compressa in Kāneʻohe Bay.Item Activity as a proxy to estimate metabolic rate and to partition the metabolic cost of diving vs. breathing in pre- and post-fasted Steller sea lions(Inter-Research Science Publisher, 2013-04-30) Fahlman, Andreas; Svärd, C.; Rosen, D. A. S.; Wilson, R. P.; Trites, AndrewThree Steller sea lions Eumetopias jubatus, trained to dive voluntarily to depths ranging from 10 to 50 m, were used to determine whether the relationship between activity and metabolic rate during a diving interval (MRDI, dive + surface interval) was affected by fasting (9 d) during the breeding season (spring through summer). We subsequently used the relationship between activity and MRDI to partition the metabolic costs between underwater breath-holding activity and surface breathing activities. We estimated activity from overall dynamic body acceleration (ODBA) measured using a 3-axis accelerometer, and measured MRDI using flow-through respirometry. The relationship between ODBA-based activity and MRDI was not affected by fasting period, suggesting that ODBA can be used to predict energy expenditure regardless of nutritional state in the spring and summer. However, the relationship between ODBA and dive metabolic rate differs from the relationship between ODBA and the surface metabolic rate before diving. Partitioning MRDI into the metabolic cost of remaining at the surface versus swimming underwater suggests that the metabolic cost of diving for Steller sea lions is approximately 29% lower than when breathing at the surface. ODBA appears to be a reasonable proxy to estimate metabolic rate in marine mammals, but more detailed behavioral data may be required to accurately apply the method in the field.Item Air-water exchange and distribution pattern of organochlorine pesticides in the atmosphere and surface water of the open Pacific ocean(Elsevier, 2020-07-02) Li, Yali; Lohmann, Rainer; Zou, Xinqing; Wang, Chenglong; Zhang, LinSurface seawater and lower atmosphere gas samples were collected simultaneously between 18°N and 40°S in the open Pacific Ocean in 2006–2007. Samples were analyzed for organochlorine pesticides (OCPs) to assess their distribution patterns, the role of ocean in the long-range transport (LRT), and the air-water exchange directions in the open Pacific Ocean. Such open ocean studies can yield useful information such as establishing temporal and spatial trends and assessing primary vs secondary emissions of legacy OCPs. Target compounds included hexachlorocyclohexanes (HCHs), dichlorodiphenyltrichloroethanes (DDTs) and its derivatives, and chlordane compounds. Concentrations for α-HCH, γ-HCH, trans-chlordane (TC), and cis-chlordane (CC) were higher in the Northern Hemisphere (NH) than the Southern Hemisphere (SH) in both gaseous and dissolved phases, while the distribution patterns of DDTs and heptachlor exo-epoxide (HEPX) showed a reversed pattern. In the N Pacific, concentrations of α-HCH and γ-HCH in the present work were lower by 63 and 16 times than those observed in 1989–1990. The distribution patterns of DDT suggested there was usage in the SH around 2006. Calculated fugacity ratios suggested that γ-HCH was volatilizing from surface water to the atmosphere, and the air-water exchange fluxes were 0.3–11.1 ng m−2 day−1. This is the first field study that reported the open Pacific Ocean has become the secondary source for γ-HCH and implied that ocean could affect LRT of OCPs by supplying these compounds via air-sea exchange.Item Amage imajimai sp. nov., a new species of Ampharetidae (Annelida: Polychaeta) from Japanese waters(European Journal Of Taxonomy, 2015-11-19) Reuscher, MichaelA new polychaete species of the family Ampharetidae, Amage imajimai sp. nov., is described from deep waters of Sagami Bay, Japan. It is characterized by the possession of four pairs of branchiae, twelve thoracic uncinigers, eleven abdominal uncinigers, and the lack of thoracic notopodial cirri. The new species is named in honor of the renowned Japanese polychaetologist Minoru Imajima. An identification key for all Amage species from Japanese waters is provided.Item Analyses of biological communities and development of indices of biotic integrity for monitoring tidal streams along the upper Texas coast(2020-05) Margo, Abraham; Pollack, Jennifer Beseres; Withers, Kim; Tolan, JamesTidal streams along the upper Texas coast are characterized by large heterogeneity in abiotic conditions and biotic communities, posing challenges to managers seeking to assess their ecological condition and develop effective management strategies. There is currently no standardized protocol for assessing ecological condition in Texas tidal stream systems. The goal of the current study was to create multimetric indices of biotic integrity (IBIs) from nekton and benthic macroinfaunal community metrics that were effective in discriminating between degraded “test” and non-degraded “reference” streams (classified by watershed land-cover data). Fifteen tidal streams were sampled twice per year in 2018 and 2019 to assess water quality, nekton, and benthic macroinfaunal dynamics. In order to create the multimetric indices of biotic integrity, multiple univariate metrics were assessed to determine the extent to which they differentiated between test and reference sites. Selected metrics were used as components in developing the multimetric IBIs, which give higher scores to samples that have similar biotic characteristics to our reference condition samples. Multivariate analyses provided a complementary approach to selection of IBI metrics by visualizing, comparing, and identifying community-level changes as well as taxa that associate with the test or reference condition. Results indicated that overall differences in biological communities between test and reference sites were often not extremely strong. Multivariate analyses indicated nekton communities exhibited stronger differentiation between test and reference samples whereas benthic macrofaunal communities were influenced more by year to year variations. However, several univariate metrics highlighted components of communities that did differ between test and reference sites, and these metrics were used to form the IBI. Comparing IBIs for both nekton and benthic macroinfauna can provide a more comprehensive understanding of biotic integrity in tidal streams than focusing on one or the other. Results should be interpreted with some caution but could help inform water resource management decisions that seek to support aquatic life use while balancing human needs for food, recreation, and industry.Item Analysing micro- and nanoplastics with cutting-edge infrared spectroscopy techniques: A critical review(2024-03-27) Xie, Junhao; Gowen, Aoife; Xu, Wei; Xu, JunliThe escalating prominence of micro- and nanoplastics (MNPs) as emerging anthropogenic pollutants has sparked widespread scientific and public interest. These minuscule particles pervade the global environment, permeating drinking water and food sources, prompting concerns regarding their environmental impacts and potential risks to human health. In recent years, the field of MNP research has witnessed the development and application of cutting-edge infrared (IR) spectroscopic instruments. This review focuses on the recent application of advanced IR spectroscopic techniques and relevant instrumentation to analyse MNPs. A comprehensive literature search was conducted, encompassing articles published within the past three years. The findings revealed that Fourier transform infrared (FTIR) spectroscopy stands as the most used technique, with focal plane array FTIR (FPA-FTIR) representing the cutting edge in FTIR spectroscopy. The second most popular technique is quantum cascade laser infrared (QCL-IR) spectroscopy, which has facilitated rapid analysis of plastic particles. Following closely is optical photothermal infrared (O-PTIR) spectroscopy, which can furnish submicron spatial resolution. Subsequently, there is atomic force microscopy-based infrared (AFM-IR) spectroscopy, which has made it feasible to analyse MNPs at the nanoscale level. The most advanced IR instruments identified in articles covered in this review were compared. Comparison metrics encompass substrates/filters, data quality, spatial resolution, data acquisition speed, data processing and cost. The limitations of these IR instruments were identified, and recommendations to address these limitations were proposed. The findings of this review offer valuable guidance to MNP researchers in selecting suitable instrumentation for their research experiments, thereby facilitating advancements in research aimed at enhancing our understanding of the environmental and human health risks associated with MNPs.Item Analysis and applications of the weighted central direction method(2016-12) Choi, HaekyoungIterative methods yield an approximated solution to a given problem by producing a sequence of points that converges to the exact solution. Due to the effectiveness of these methods, they become one of the core mathematical procedures widely used in many major mathematical areas such as Differential Equations, Linear Algebra, and Matrix Analysis. The Methods of Alternating Projection, which we will use in this thesis, form a class of iterative methods based on the relevant projection algorithm introduced by John von Neumann. This outstanding algorithm received considerable attention by mathematicians which contributed to a number of different algorithms to solve several problems. Recently, two former graduate students at Texas A&M University-Corpus Christi, Melina Wijaya and Zulema Cervantes, introduced a couple of new algorithms in this area. Wijaya presented the Weighted Direction algorithm, and Cervantes introduced the Weighted Central Direction algorithm by combining the Weighted Direction and the Central Direction. The algorithm with the combination of two directions achieved a faster convergence than the algorithm with the Weighted Direction only. However, the Weighted Central Direction algorithm needs a parameter which depends on the size of the problems. This thesis carries two objectives. Firstly, study the role of the wide angle condition which guarantees the convergence in the Weighted Direction algorithm in order to analyze if this condition is necessary for the convergence of the algorithm. Secondly, improve the algorithms developed by Wijaya and Cervantes in order to obtain a faster convergence by finding an adequate ratio between the Weighted Direction and the Central Direction that is independent of the size of the problems.Item An analysis of emergency management agencies gis data for planning 9-1-1 services for the border counties of the lower Rio Grande Valley(2017-08) Nino, Orlando; Smith, Richard; Jeffress, Gary; Huang, YuxiaTexas 9-1-1 entities collect data that can be used to gain knowledge on 9-1-1 call patterns and trends. It is ideal to know these issues too efficiently maximize monies appropriated to local emergency management agencies. This research will analyze 9-1-1 calls and two police departments calls for service using Geographic Information Science (GIS). This information provided by multiple emergency management agencies to better plan 9-1-1 services in the border counties of the Rio Grande Valley. The data that was used is recorded daily by these agencies. Many emergency management organizations keep their own GIS data in-house and they need to be analyzed with 9-1-1 data. Analyzing various GIS databases can yield better results, in finding correlation within each dataset, hotspots and inadequate data collection. These results can then be used by the organizations that contributed the data and shared to all stakeholders.Item Analysis of the vcgC gene in Vibrio vulnificus isolates from the Texas Coastal Bend region of the Gulf of Mexico(2023-05-12) Buck, Gregory W; Brumfield, LarReshia I; Giagnocavo, Stephanie Dudics; Perkins, Danielle S; Tortosa, Alvaro Ortola; Okuyemi, Tolulope B; Carbaugh, Joshua S; Planas Costas, Githzette M; Ramirez, Gabriel DVibrio vulnificus is a gram-negative, halophilic bacterium normally found in temperate marine and estuarine waters. The organism may enter wounds in the skin and cause sepsis or necrotizing fasciitis; the latter condition has a 50-60% mortality rate and may result in death or disfigurement within 4-6 days. Persons exposed to coastal flood waters during hurricanes may be at risk for this organism. The virulence-correlated gene, vcgC, is specific for clinical isolates of V. vulnificus, but the function of this locus remains unknown. This study used Polymerase Chain Reaction (PCR) and novel primers for vcgC not previously described to specifically identify V. vulnificus isolates from the Texas Coastal Bend region that may result in serious infections. Of the 28 isolates, four isolates could not be revived multiple times; crude lysates of the remaining 24 Vibrio vulnificus cultures were analyzed by PCR, and 19 were found to have amplicons of 428bp for vcgC. This study confirms the presence of the vcgC gene in V. vulnificus isolates from the Texas Coastal Bend region of the Gulf of Mexico.Item Analytic solutions for the harmonic potentials involving concentric layered dielectric spheres(2018-05) Cisneros, Frank; Palaniappan, Devanayagam; Sadovski, Alexey L.; Zimmer, BeateThe mathematical problem of a conducting spherical core of radius 𝑎 concentrically covered by a dielectric phase of radius 𝑏 placed in an arbitrary external electric field is investigated. The vector field equations for the electric field (Maxwell equations) and the boundary conditions are transformed to a scalar boundary value problem (BVP) in terms of the harmonic potential functions. The harmonic potentials denoted by Φ𝐼(𝑟,𝜃,𝜙) and Φ𝐼𝐼(𝑟,𝜃,𝜙) where (𝑟,𝜃,𝜙) are spherical coordinates, satisfy the Laplace equations in the regions 𝑏<𝑟 and 𝑎 < 𝑟 < 𝑏, respectively. General analytical solutions for the potentials in the two phases are determined in infinite series form using spherical harmonics methods. Exact closed form solutions are also derived via an alternative approach. The latter solutions contain integrals involving harmonic functions. Our general solutions are applicable for arbitrary external potentials disturbed by a conducting spherical core with a dielectric coating. Several illustrative examples are investigated and exact solutions for them are constructed using our general solutions. The non-dimensional parameter 𝑘= 𝜀𝐼/(𝜀𝐼+𝜀𝐼𝐼) , where 𝜀𝐼 is the dielectric constant for the region 𝑟 > 𝑏 and 𝜀𝐼𝐼 is the dielectric constant for the region 𝑎 < 𝑟 < 𝑏, influences the potential patterns in the case of externally imposed constant and linear fields. Our results for the source induced field indicate that the force is positive or negative depending on 𝑘 < 0.5 or 𝑘 > 0.5. Furthermore, the force is greater than zero when the core radius 𝑎 approaches the value of the outer radius 𝑏. We believe that our mathematical results are of interest where coated dielectric objects are exposed to external electric fields.Item Anemonefish Genomics(2022) Salamin, Nicolas; Schunter, Celia; Monroe, Alison; Ryu, Taewoo; Ravasi, TimothyAnemonefish consists of 30 species and are likely the most recognizable fishes to the public due to their unique colour patterns, easy captive breeding, and the animation film Finding Nemo. They are also important species to biologists owing to their symbiotic relationship with anemones as well as sequential hermaphroditism and hence serve as emerging model organisms in ecology, evolution, and development. The latest advancements in high-throughput sequencing technologies and bioinformatic analysis have facilitated studies in anemonefish research. In this chapter, we first show the recent genomics studies that unveil the genomic architecture and underlying evolutionary processes in anemonefish. We also cover how state-of-the-art transcriptomic and proteomic techniques have been utilized to capture and uncover the fundamental molecular mechanisms driving dynamic changes in biological processes throughout development and under various environmental changes.Item Anthropogenic effects on the marine environment adjacent to Palmer Station, Antarctica(Cambridge, 2021-12-07) Palmer, Terence A.; Klein, Andrew; Sweet, Stephen; Montagna, Paul; Hyde, Larry; Wade, Terry; Pollack, Jennifer BeseresLocalized contamination from research-related activities and its effects on macrofauna communities in the marine environment were investigated at Palmer Station, a medium-sized Antarctic research station. Relatively low concentrations of polycyclic aromatic hydrocarbons (PAHs; 32–302 ng g-1) and total petroleum hydrocarbons (TPHs; 0.9–8.9 μg g-1) were detected in sediments adjacent to the sewage outfall and pier, where most human activities were expected to have occurred, and at even lower concentrations at two seemingly reference areas (PAHs 6–30 ng g-1, TPHs 0.03–5.1 μg g-1). Elevated concentrations of PAHs in one sample taken in one reference area (816 ng g-1) and polychlorinated biphenyls (353 ng g-1) and dichloro-diphenyl-trichloroethane (3.2 and 25.3 ng g-1) in two samples taken adjacent to the sewage outfall indicate spatial heterogeneity of localized sediment contamination. Limpet (Nacella concinna) tissues collected adjacent to Palmer Station had high concentrations of PAHs, copper, lead, zinc and several other metals relative to outlying islands. Sediment and limpet tissue contaminant concentrations have decreased since the early 1990s following the Bahía Paraíso spill. Natural sediment characteristics affected macrofaunal community composition more than contamination adjacent to Palmer Station, presumably because of the low overall contamination levels.Item Applicability of the microfragmentation technique to propagate corals in a fisherfolk community in the Philippines(2019-12) Broquet, Nicole C.; Scarpa, John; Siccardi, Anthony; Pollack, Jennifer Beseres; Vaughan, DavidCoral nursery implementation is becoming a highly prevalent method of coral restoration in the Philippines. These nurseries primarily focus on fast-growing branching corals and do not commonly include massive corals. This is due to the slow growth rate and morphology of these corals, which are not conducive to traditional nursery methods. Microfragmentation is a relatively new technique that has displayed positive results for massive coral propagation. This method utilizes small coral fragments (≈1-3 cm) that are mounted on platforms, then placed in ex-situ or in-situ nurseries. The fragments exhibit rapid growth, which decreases the duration of the nursery phase before transplantation. Though microfragmentation is becoming more practiced, there is no published literature specifically focused on this method in the Philippines. The present study aimed to determine if: 1) coral specimen (i.e., putative genotype) significantly influenced growth, and 2) this method was viable in a fisherfolk community in the Western Visayas of the Philippines. Five corals of opportunity (putative genotypes) of the lobe coral, Porites lobata, were fragmented with hammer and chisel by several volunteer fisherfolk. The fragments were cultured from April-August 2018 in an in-situ fixed-leg nursery at a depth of approximately 2m. Maintenance was performed weekly and measurements of growth (i.e., volume change) were conducted monthly. The fragments were then transplanted to a selected restoration site and monitored for one month. A hierarchical Bayesian log-linear regression model indicated that 59.7% of growth (volume change) variation was attributed to coral specimen (i.e., putative genotype) and 26.4% of growth variation was attributed to the individual fragment. Overall, the average monthly increase in particular specimen’s fragment volume was 23.5% per month (95% CI, 3.43% - 43.9%/month) with the greatest monthly increase for a specimen at 30.1% per month (95% CI, 19.3 – 40.3%/month). Mean tissue spreading was determined to be 43.24cm2 /month (95% CI 44.5 – 79.4 cm2 /month) and mean linear extension was estimated to be 1.55 cm/month (95% CI, 0.92 – 2.02 cm/yr). Though high growth rates for P. lobata were documented in this study, nursery maintenance was significant due to lack of resources and location of nursery. This method may be viable and highly beneficial in established coral nurseries in the Philippines, but may not be feasible in a remote fisherfolk communityItem Applying segmentation and neural networks to detect and quantify marine debris from aerial images captured by unmanned aerial system and mobile device(2018-08) Tran, Kieu; Conkle, Jeremy; Starek, Michael J.; Gibeaut, JamesMarine debris is a global issue with adverse impacts on the marine environment, wildlife, economy, and human health. Its presence on beaches may vary due to topography, hydrological conditions, proximity to litter sources, and the extent of beach use. Studies of these parameters on beach litter are essential for understanding spatial and temporal patterns; however, this work is labor-intensive and time-consuming. To overcome these obstacles while gaining higher spatial and temporal resolution data, two methods were developed (1) segmentation and (2) regions with convolutional neural networks (R-CNN) to detect and quantify marine macro-debris using high-resolution imagery. Data to develop and test the methods were collected using a small rotary Unmanned Aerial System (UAS) with an RGB sensor at various altitudes over a 100m section of sandy beach of Mustang Island, Texas. Images were processed through structure-from-motion photogrammetry to derive orthomosaics for each flight. Orthomosaics were then run through an image processing, and classification workflow developed for segmentation and delineation of imaged debris. The segmentation algorithm detected the most debris at the lowest altitude (215 of 341 total at 15m), with decreasing detections at 22m (101) and 35m (50). The second method applied deep learning object detection to smartphone images. Based on the dataset and the network architecture, R-CNN mean average precision can range from 31.4% to 66% (Girshick et al., 2014). Training for R-CNN consisted of three stages: extract region proposals, train AlexNet to classify objects, and train a bounding box regression model to locate the debris. Average precision for the Specifically Engineered Algorithm for Gathering and Understanding Litter Location (SEAGULL) detector was ~22%, meaning it has a low performance at detecting all the debris in the testing dataset and correctly predicting whether or not that region was debris or not. Object detection has been a challenging task for decades, and with a low overall debris detection accuracy, it needs to be further improved with the use of a larger dataset or adjusting the training parameters. Few studies have been published on this topic, but this work demonstrates that remote sensing with UAS has the potential to increase research efficiency.