Same species, different population dynamics: Spatio-temporal differences of Undaria pinnatifida (Ochrophyta, Phaeophyceae) in the intertidal of North Patagonia, Argentina.

Population dynamics can be influenced by physical and biological factors, particularly in stressful environments. Introduced species usually have great physiological plasticity, resulting in populations with different traits. Undaria pinnatifida, a macroalga originally described from northeast Asia, was introduced in Northern Patagonia, Argentina (San Matías Gulf) around 2010. To describe the spatio-temporal variability in population structure and morphometry of U. pinnatifida, we conducted monthly field samplings for 2 years at the intertidal area of two contrasting sites in the San Matías Gulf. Individuals of U. pinnatifida were classified by developmental stage, and their morpho-gravimetric variables were measured. In both intertidal sites juveniles were found in higher proportion during austral autumn and grew and matured during the autumn-winter months (from May onwards), and individuals senesced during early austral summer (December and January). Conversely, density and biomass were largely different between sites, and individuals showed slight morphological variability between sites. Environmental (e.g., nutrient concentration, available substrate) and biological factors (e.g., facilitation, competition) may explain the observed differences. Since there is not a macroalga with U. pinnatifida morphometrical characteristics in the intertidal environments of San Matías Gulf, studying this recent introduction gives us a better understanding of its potential ecological effects.

Practical application of a Bayesian network approach to poultry epigenetics and stress.

BACKGROUND: Relationships among genetic or epigenetic features can be explored by learning probabilistic networks and unravelling the dependencies among a set of given genetic/epigenetic features. Bayesian networks (BNs) consist of nodes that represent the variables and arcs that represent the probabilistic relationships between the variables. However, practical guidance on how to make choices among the wide array of possibilities in Bayesian network analysis is limited. Our study aimed to apply a BN approach, while clearly laying out our analysis choices as an example for future researchers, in order to provide further insights into the relationships among epigenetic features and a stressful condition in chickens (Gallus gallus). RESULTS: Chickens raised under control conditions (n = 22) and chickens exposed to a social isolation protocol (n = 24) were used to identify differentially methylated regions (DMRs). A total of 60 DMRs were selected by a threshold, after bioinformatic pre-processing and analysis. The treatment was included as a binary variable (control = 0; stress = 1). Thereafter, a BN approach was applied: initially, a pre-filtering test was used for identifying pairs of features that must not be included in the process of learning the structure of the network; then, the average probability values for each arc of being part of the network were calculated; and finally, the arcs that were part of the consensus network were selected. The structure of the BN consisted of 47 out of 61 features (60 DMRs and the stressful condition), displaying 43 functional relationships. The stress condition was connected to two DMRs, one of them playing a role in tight and adhesive intracellular junctions in organs such as ovary, intestine, and brain. CONCLUSIONS: We clearly explain our steps in making each analysis choice, from discrete BN models to final generation of a consensus network from multiple model averaging searches. The epigenetic BN unravelled functional relationships among the DMRs, as well as epigenetic features in close association with the stressful condition the chickens were exposed to. The DMRs interacting with the stress condition could be further explored in future studies as possible biomarkers of stress in poultry species.

Possible female philopatry of the smooth hammerhead shark Sphyrna zygaena revealed by genetic structure patterns.

We assessed the spatial pattern of genetic structure of smooth hammerhead shark Sphyrna zygaena in 10 localities from the Northern Mexican Pacific. A total of 35 haplotypes were identified in 129 sequences of the mtDNA control region. The results showed slight but significant genetic structure among localities (ΦST = 0.044, P < 0.001). In addition, the localities with highest number of juveniles were genetically different (ΦST = 0.058, P < 0.024), which may be representative of nursery areas. The genetic differentiation pattern can be associated to female philopatry and preference for particular birthing sites. Finally, historical demography shows that S. zygaena populations present a recent demographic expansion that occurred during glacial events in the late Pleistocene to early Holocene.

A two-step Bayesian network approach to identify key SNPs associated to multiple phenotypic traits in four purebred laying hen lines.

When purebred laying hen chicks hatch, they remain at a rearing farm until approximately 17 weeks of age, after which they are transferred to a laying farm. Chicks or pullets are removed from the flocks during these 17 weeks if they display any rearing abnormality. The aim of this study was to investigate associations between single nucleotide polymorphisms (SNPs) and rearing success of 4 purebred White Leghorns layer lines by implementing a Bayesian network approach. Phenotypic traits and SNPs of four purebred genetic White Leghorn layer lines were available for 23,000 rearing batches obtained between 2010 and 2020. Associations between incubation traits (clutch size, embryo mortality), rearing traits (genetic line, first week mortality, rearing abnormalities, natural death, rearing success, pullet flock age, and season) and SNPs were analyzed, using a two-step Bayesian Network (BN) approach. Furthermore, the SNPs were connected to their corresponding genes, which were further explored in bioinformatics databases. BN analysis revealed a total of 28 SNPs associated with some of the traits: ten SNPs were associated with clutch size, another 10 with rearing abnormalities, a single SNP with natural death, and seven SNPs with first week mortality. Exploration via bioinformatics databases showed that one of the SNPs (ENAH) had a protein predicted network composed of 11 other proteins. The major hub of this SNP was CDC42 protein, which has a role in egg production and reproduction. The results highlight the power of BNs in knowledge discovery and how their application in complex biological systems can help getting a deeper understanding of functionality underlying genetic variation of rearing success in laying hens. Improved welfare and production might result from the identified SNPs. Selecting for these SNPs through breeding could reduce stress and increase livability during rearing.

Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series.

A curated database of shark and ray biological data is increasingly necessary both to support fisheries management and conservation efforts, and to test the generality of hypotheses of vertebrate macroecology and macroevolution. Sharks and rays are one of the most charismatic, evolutionary distinct, and threatened lineages of vertebrates, comprising around 1,250 species. To accelerate shark and ray conservation and science, we developed Sharkipedia as a curated open-source database and research initiative to make all published biological traits and population trends accessible to everyone. Sharkipedia hosts information on 58 life history traits from 274 sources, for 170 species, from 39 families, and 12 orders related to length (n = 9 traits), age (8), growth (12), reproduction (19), demography (5), and allometric relationships (5), as well as 871 population time-series from 202 species. Sharkipedia relies on the backbone taxonomy of the IUCN Red List and the bibliography of Shark-References. Sharkipedia has profound potential to support the rapidly growing data demands of fisheries management, international trade regulation as well as anchoring vertebrate macroecology and macroevolution.

A biologging database of juvenile white sharks from the northeast Pacific.

Species occurrence records are vital data streams in marine conservation with a wide range of important applications. From 2001-2020, the Monterey Bay Aquarium led an international research collaboration to understand the life cycle, ecology, and behavior of white sharks (Carcharodon carcharias) in the southern California Current. The collaboration was devoted to tagging juveniles with animal-borne sensors, also known as biologging. Here we report the full data records from 59 pop-up archival (PAT) and 20 smart position and temperature transmitting (SPOT) tags that variously recorded pressure, temperature, and light-level data, and computed depth and geolocations for 63 individuals. Whether transmitted or from recovered devices, raw data files from successful deployments (n = 70) were auto-ingested from the manufacturer into the United States (US) Animal Telemetry Network's (ATN) Data Assembly Center (DAC). There they have attributed a full suite of metadata, visualized within their public-facing data portal, compiled for permanent archive under the DataONE Research Workspace member node, and are accessible for download from the ATN data portal.

Fisheries interactions and the challenges for target and nontargeted take on shark conservation in the Mexican Pacific.

Sharks have been of great cultural and socioeconomic importance in Mexico since the late 19th century, when the first fisheries were prosecuted in the Gulf of California to export fins to China. Mexican shark and ray fisheries are classified mainly by the size of the fishing vessel and include small- (7.5-10m), medium- (10-27m), and large-sized (>27m) fisheries. All are multispecies fisheries that use longline or gillnet gear, with their relative productivity varying over time. Off the Pacific coast, early shark small size vessel fisheries in the Gulf of California were driven by the need for vitamin A from livers, especially during World War II. As this fishery declined, new shark fishing opportunities arose because of government support and the development of the medium-sized fishery, which was capable of farther offshore excursions. Shark meat became an important part of the diets of poor and impoverished citizens during the 1950s and 1960s. The establishment of a Mexican Exclusive Economic Zone in 1976 pushed foreign vessels from Asia out of Mexican waters and led to the development of the large-sized vessel fishery to exploit pelagic sharks in offshore waters. By the early 1980s, Mexico shark fisheries were among the most productive in the world; however, a national economic crisis reduced effort and landings until the late 1980s, when several new fisheries emerged. Landings from Pacific states fluctuated between ~13,000 and 24,000t (dressed weight) during 1987-2012 but expanded steadily thereafter because of government support and offshore fleet expansion. Shark fisheries landings from the Mexican Pacific are currently at their highest recorded levels, exceeding 31,000t; however, a lack of species-specific landings and life history information has precluded population assessments of targeted stocks. In addition, though several recent management measures have been enacted to protect Mexican shark and ray fishery resources, the enforcement of these regulations is severely lacking. Therefore, the long-term sustainability of current fishing levels is unknown but should engender concern based on anecdotal evidence of serial depletion among historical elasmobranch targets in the Mexican Pacific.

Biodiversity and conservation of sharks in Pacific Mexico.

Mexico is home to a broad biodiversity of shark species, and more than half of the sharks in Mexican waters are distributed in the Mexican Pacific, with over 62 species recorded. This high biodiversity is the result of numerous and diverse marine and coastal environments, including the dynamic Mexican seas, where circulation and spatial variation of oceanic currents is complex, and the seasonal variation of isotherms can be substantial. In the Mexican Pacific we can distinguish some patterns of species distribution, with temperate water and subtropical species found in the northern regions, and tropical conditions and species found in the south. Due to the blending of cold and warm waters, however, we can find a mixture of subtropical and tropical sharks in northern regions seasonally, off the west coast of the Baja California Peninsula and in the Gulf of California, and these areas contain the highest shark species richness. In this chapter we described the shark species biodiversity occurring in the Mexican Pacific, review their conservation status in a regional and global context, and summarize the main conservation measures and issues associated with their management.

The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research.

Integration of open access, curated, high-quality information from multiple disciplines in the Life and Biomedical Sciences provides a holistic understanding of the domain. Additionally, the effective linking of diverse data sources can unearth hidden relationships and guide potential research strategies. However, given the lack of consistency between descriptors and identifiers used in different resources and the absence of a simple mechanism to link them, gathering and combining relevant, comprehensive information from diverse databases remains a challenge. The Open Pharmacological Concepts Triple Store (Open PHACTS) is an Innovative Medicines Initiative project that uses semantic web technology approaches to enable scientists to easily access and process data from multiple sources to solve real-world drug discovery problems. The project draws together sources of publicly-available pharmacological, physicochemical and biomolecular data, represents it in a stable infrastructure and provides well-defined information exploration and retrieval methods. Here, we highlight the utility of this platform in conjunction with workflow tools to solve pharmacological research questions that require interoperability between target, compound, and pathway data. Use cases presented herein cover 1) the comprehensive identification of chemical matter for a dopamine receptor drug discovery program 2) the identification of compounds active against all targets in the Epidermal growth factor receptor (ErbB) signaling pathway that have a relevance to disease and 3) the evaluation of established targets in the Vitamin D metabolism pathway to aid novel Vitamin D analogue design. The example workflows presented illustrate how the Open PHACTS Discovery Platform can be used to exploit existing knowledge and generate new hypotheses in the process of drug discovery.

Scientific competency questions as the basis for semantically enriched open pharmacological space development.

Molecular information systems play an important part in modern data-driven drug discovery. They do not only support decision making but also enable new discoveries via association and inference. In this review, we outline the scientific requirements identified by the Innovative Medicines Initiative (IMI) Open PHACTS consortium for the design of an open pharmacological space (OPS) information system. The focus of this work is the integration of compound-target-pathway-disease/phenotype data for public and industrial drug discovery research. Typical scientific competency questions provided by the consortium members will be analyzed based on the underlying data concepts and associations needed to answer the questions. Publicly available data sources used to target these questions as well as the need for and potential of semantic web-based technology will be presented.