A new approach to the solution of the linear mixing model for a single isotope: application to the case of an opportunistic predator

Interpretation of southern hemisphere humpback whale diet via stable isotopes; implications of tissue-specific analysis

Blubber and skin are commonly used tissues in stable isotope analysis for the purpose of investigating cetacean diet. Critical comparison of tissue-specific isotopic signals is, however, lacking resulting in uncertainty surrounding the representativeness and therefore utility of different tissues for accurate determination of recent foraging. This study used remotely biopsied blubber and skin tissues from southern hemisphere humpback whales for strategic comparison of δ13C and δ15N values. Samples were collected between 2008-2018 as part of long-term monitoring under the Humpback Whale Sentinel Program. Blubber tissues were lipid-extracted prior to analysis, whilst mathematical lipid-correction was performed on skin samples. Isotopic values from paired blubber and skin samples from the same individuals were compared to assess whether tissues could be used interchangeably for isotope analysis and dietary interpretation. Significant differences were observed for both δ13C and δ15N, flagging previously undocumented methodological considerations, and the need for method validation and standardisation in application of these approaches. This study therefore advances methodological aspects of cetacean dietary analysis. This is of elevated importance in the context of rapidly changing ocean ecosystems.

Tracing the predominant sources of carbon in PM2.5 using δ13C values together with OC/EC and select inorganic ions over two COALESCE locations

As part of the COALESCE (Carbonaceous Aerosol Emissions, Source apportionment and Climate Impacts) campaign, ambient PM_2.5 was collected at two regional sites (Bhopal and Mysuru) in India during 2019. We utilized organic carbon (OC), elemental carbon (EC) and water-soluble inorganic ions together with δ¹³C values, to better understand total carbon (TC) sources at these locations. The annual average δ¹³C values (-26.2 ± 0.6‰) at Mysuru and Bhopal (-26.6 ± 0.6‰) were comparable. However, at Mysuru, except during winter, day-to-day variability was much lower (narrow range of -26.8 to -26.0‰) than that at Bhopal (range: -28.1 to -24.7‰), suggesting that TC was contributed by few sources, likely dominated by vehicular emissions. Seasonal average δ¹³C values at Bhopal increased slightly (-25.8 ± 0.5‰) during the winter (Jan-Feb) and decreased (-27.0 ± 0.3‰) during the monsoon (Jun-Sep) season compared to the annual average. The decrease in δ¹³C values during the monsoon season was likely driven by enhanced secondary organic aerosol formation. Further, based on MODIS derived fire spots and back trajectories, we infered that the δ¹³C values (-27.5 to -26.0‰) in Bhopal during the post-monsoon season (Oct-Dec) were indicative of dominant biomass burning contributions. The inorganic ions/TC ratio during this season suggested that biomass burning aerosol was aged and may have been transported from crop residue burning in the Indo-Gangetic plains. At Mysuru, like the trend at Bhopal, the δ¹³C values during the monsoon season were lower than those during the winter season. Finally, δ¹³C values were input to a Bayesian model-MixSIAR to demonstrate the usefulness of such models in apportioning TC. In its simplest implementation, the model separated TC sources into fossil fuel emissions and non-fossil fuel sources . Fossil fuel combustion emissions accounted for 47 ± 19% and 62 ± 22% of the TC at Bhopal and Mysuru, respectively.

Application of a Deep Matrix Factorization Model on Integrated Gene Expression Data

Background:

Non-negative Matrix Factorization (NMF) has been extensively used in gene expression data. However, most NMF-based methods have single-layer structures, which may achieve poor performance for complex data. Deep learning, with its carefully designed hierarchical structure, has shown significant advantages in learning data features.

Objective:

In bioinformatics, on the one hand, to discover differentially expressed genes in gene expression data; on the other hand, to obtain higher sample clustering results. It can provide the reference value for the prevention and treatment of cancer.

Method:

In this paper, we apply a deep NMF method called Deep Semi-NMF on the integrated gene expression data. In each layer, the coefficient matrix is directly decomposed into the basic and coefficient matrix of the next layer. We apply this factorization model on The Cancer Genome Atlas (TCGA) genomic data.

Results:

The experimental results demonstrate the superiority of Deep Semi-NMF method in identifying differentially expressed genes and clustering samples.

Conclusion:

The Deep Semi-NMF model decomposes a matrix into multiple matrices and multiplies them to form a matrix. It can also improve the clustering performance of samples while digging out more accurate key genes for disease treatment.

Leopard seal diets in a rapidly warming polar region vary by year, season, sex, and body size

Background

Resolving the preferred prey items and dietary proportions of leopard seals is central to understanding food-web dynamics in the rapidly-warming Antarctic Peninsula region. Previous studies have identified a wide range of prey items; however, due to anecdotal or otherwise limited information, leopard seal diets remain unresolved by seal sex, individual, body size, region, and season. Over the 2013, 2014, and 2017 field seasons we collected scat, tissue samples (red blood cells and plasma; n = 23) for stable isotope analyses, and previously-reported animal-borne video from 19 adult leopard seals foraging near mesopredator breeding colonies at Cape Shirreff, Livingston Island. We summarized a priori diet information from scat and video analysis and applied a three-isotope (δ¹³C, δ¹⁵N, δ³⁴S), four-source (fish, fur seal, krill, penguin) Bayesian mixing model to examine temporal variability in both prey sources and leopard seal tissues.

Results

The austral spring diets of males and females focused on Antarctic krill (31.7–38.0%), notothen fish (31.6–36.5%), and penguin (24.4–26.9%) and were consistent across all 3 years. Several lines of evidence suggest the transition to summer foraging was distinct for males and females. Female diets transitioned rapidly to higher δ¹⁵N values (+2.1‰), indicating increased consumption of penguin (29.5–46.2%) and energy-dense Antarctic fur seal pup (21.3–37.6%).

Conclusions

The seasonal increase in leopard seal δ¹⁵N values, and thus fur seal in their diet, was predictably related to larger body size; it may also be forcing reductions to the largest Antarctic fur seal colony in the Antarctic Peninsula. Our ensemble sampling approach reduces historical biases in monitoring marine apex predator diets. Further, our results are necessary to best inform regional fisheries management planning.

Radiocarbon as a Novel Tracer of Extra-Antarctic Feeding in Southern Hemisphere Humpback Whales

Bulk stable isotope analysis provides information regarding food web interactions, and has been applied to several cetacean species for the study of migration ecology. One limitation in bulk stable isotope analysis arises when a species, such as Southern hemisphere humpback whales, utilises geographically distinct food webs with differing isotopic baselines. Migrations to areas with different baselines can result in isotopic changes that mimic changes in feeding relations, leading to ambiguous food web interpretations. Here, we demonstrate the novel application of radiocarbon measurement for the resolution of such ambiguities. Radiocarbon was measured in baleen plates from humpback whales stranded in Australia between 2007 and 2013, and in skin samples collected in Australia and Antarctica from stranded and free-ranging animals. Radiocarbon measurements showed lower values for Southern Ocean feeding than for extra-Antarctic feeding in Australian waters. While the whales mostly relied on Antarctic-derived energy stores during their annual migration, there was some evidence of feeding within temperate zone waters in some individuals. This work, to our knowledge, provides the first definitive biochemical evidence for supplementary feeding by southern hemisphere humpback whales within temperate waters during migration. Further, the work contributes a powerful new tool (radiocarbon) for tracing source regions and geographical feeding.

Isotopic Evidence of a Wide Spectrum of Feeding Strategies in Southern Hemisphere Humpback Whale Baleen Records

Our current understanding of Southern hemisphere humpback whale (Megaptera novaeangliae) ecology assumes high-fidelity feeding on Antarctic krill in Antarctic waters during summer, followed by fasting during their annual migration to and from equatorial breeding grounds. An increase in the number of reported departures from this feeding/fasting model suggests that the current model may be oversimplified or, alternatively, undergoing contemporary change. Information about the feeding and fasting cycles of the two Australian breeding populations of humpback whales were obtained through stable isotope analysis of baleen plates from stranded adult individuals. Comparison of isotope profiles showed that individuals from the West Australian breeding population strongly adhered to the classical feeding model. By contrast, East Australian population individuals demonstrated greater heterogeneity in their feeding. On a spectrum from exclusive Antarctic feeding to exclusive feeding in temperate waters, three different strategies were assigned and discussed: classical feeders, supplemental feeders, and temperate zone feeders. Diversity in the inter-annual feeding strategies of humpback whales demonstrates the feeding plasticity of the species, but could also be indicative of changing dynamics within the Antarctic sea-ice ecosystem. This study presents the first investigation of trophodynamics in Southern hemisphere humpback whales derived from baleen plates, and further provides the first estimates of baleen plate elongation rates in the species.

Best practices for use of stable isotope mixing models in food-web studies

Stable isotope mixing models are increasingly used to quantify consumer diets, but may be misused and misinterpreted. We address major challenges to their effective application. Mixing models have increased rapidly in sophistication. Current models estimate probability distributions of source contributions, have user-friendly interfaces, and incorporate complexities such as variability in isotope signatures, discrimination factors, hierarchical variance structure, covariates, and concentration dependence. For proper implementation of mixing models, we offer the following suggestions. First, mixing models can only be as good as the study and data. Studies should have clear questions, be informed by knowledge of the system, and have strong sampling designs to effectively characterize isotope variability of consumers and resources on proper spatio-temporal scales. Second, studies should use models appropriate for the question and recognize their assumptions and limitations. Decisions about source grouping or incorporation of concentration dependence can influence results. Third, studies should be careful about interpretation of model outputs. Mixing models generally estimate proportions of assimilated resources with substantial uncertainty distributions. Last, common sense, such as graphing data before analyzing, is essential to maximize usefulness of these tools. We hope these suggestions for effective implementation of stable isotope mixing models will aid continued development and application of this field.

Source partitioning using stable isotopes: coping with too much variation

Background

Stable isotope analysis is increasingly being utilised across broad areas of ecology and biology. Key to much of this work is the use of mixing models to estimate the proportion of sources contributing to a mixture such as in diet estimation.

Methodology

By accurately reflecting natural variation and uncertainty to generate robust probability estimates of source proportions, the application of Bayesian methods to stable isotope mixing models promises to enable researchers to address an array of new questions, and approach current questions with greater insight and honesty.

Conclusions

We outline a framework that builds on recently published Bayesian isotopic mixing models and present a new open source R package, SIAR. The formulation in R will allow for continued and rapid development of this core model into an all-encompassing single analysis suite for stable isotope research.

An alternative approach to reconstructing organic matter accumulation with contrasting watershed disturbance histories from lake sediments

A number of proxies, including carbon to nitrogen ratio (C:N) and stable isotopes (delta(13)C and delta(15)N), have been used to reconstruct organic matter (OM) profiles from lake sediments and these proxies individually or in combination cannot clearly discriminate different sources. Here we present an alternative approach to elucidate this problem from lake sediments as a function of watershed scale land use changes. Stable isotope signatures of defined OM sources from the study watersheds, Shawnigan Lake (SHL) and Elk Lake (ELL), were compared with sedimentary proxy records. Results from this study reveal that terrestrial inputs and catchment soil coinciding with the watershed disturbances histories probably contributed in recent trophic enrichment in SHL. In contrast, cultural eutrophication in ELL was partially a result of input from catchment soil (agricultural activities) with significant input from lake primary production as well. Results were consistent in both IsoSource (IsoSource version 1.2 is a Visual Basic program used for source separation, (http://www.epa.gov/wed/pages/models/isosource/isosource.htm) and discriminant analysis (statistical classification technique).

Trace element analysis in the serum and hair of Antarctic leopard seal, Hydrurga leptonyx, and Weddell seal, Leptonychotes weddellii

Leopard seal, Hydrurga leptonyx, and Weddell seal, Leptonychotes weddellii, occupy an upper trophic level within the Antarctic ecosystem and are useful indicator species in the Southern Ocean of trace element concentrations. Reference values for the concentration of 19 trace elements were determined in the serum and hair of leopard and Weddell seals sampled in Eastern Antarctica. These reference values can be used as 'baseline' levels for monitoring trace element concentrations in these species. Greater trace element concentrations were determined in hair compared to serum, indicating different time scales of trace element accumulation in these samples. For the majority of trace elements, except for Se in the leopard seal samples and Cr in the Weddell seal samples, significant regression relationships for trace element concentrations in hair and serum were not elucidated. Significant differences were determined in the concentrations of seven out of 15 elements with hair type, moult and new, in the leopard seal; concentrations in moult hair were determined to be greater than in new hair for all elements except Zn. Hair analysis was determined to be useful for monitoring exposure to trace elements and when collected off the ice from moulting seals, hair can be employed as a non-invasive sample for trace element analysis in leopard and Weddell seals.

What do harp seals eat? Comparing diet composition from different compartments of the digestive tract with diets estimated from stable-isotope ratios

This study compared diet reconstructed from different compartments of the digestive tract of harp seals (Pagophilus groenlandicus (Erxleben, 1777)) with the diet estimated using stable carbon and stable nitrogen isotope ratios in mixing models. Diet composition in 18 feeding harp seals (mean age = 2.4 years, SD = 1.8 years, range = 0–6 years) was determined using traditional methods of hard-part identification and reconstruction, and stable carbon and stable nitrogen isotope ratios. Diet composition consisted of 68.8% (SD = 8.7%) and 69.6% (SD = 11.6%) by mass of invertebrates or 65.0% (SD = 8.8%) and 66.5% (SD = 11.8%) by energy of invertebrates for the stomach and small-intestine compartments, respectively. Reconstructed diets using material recovered from the large-intestine contents suggested a diet of 43.1% (SD = 12.2%) and 38.0% (SD = 11.9%) invertebrates using mass and energy, respectively. Stable carbon and stable nitrogen isotope ratios determined for the same individual harp seals suggested a diet consisting of approximately 66.1% (SD = 117.4) invertebrates, indicating that diet reconstructions based on hard parts from stomachs are likely to be more representative than reconstructions from large-intestine contents. In species that feed on a combination of vertebrates and invertebrates, the use of faecal material to reconstruct diet composition will likely underestimate the importance of invertebrates in the diet.