Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss)

Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest

Internet of Things for Efficient Wildlife Conservation: Challenges and Opportunities

Danau Girang Field Centre (DGFC) is located in Sabah Malaysia. The only access to the field centre is through the river. Similarly, all the research activities are conducted by going through the river. It is worth noting that Sabah Malaysia is a high humidity region where electronic components could get damaged quite quickly due to environmental factors such as moisture. Further, in jungle terrains, insects could also get attracted to copper within electronic components. We need to keep in mind this context when we are addressing the challenges. We conducted a two full-day workshop to explore and identify research challenges that could potentially be addressed using the Internet of Things (IoT) technologies

Low-Cost SMS Driven Location Tracking Platform Towards Anti-Poaching Efforts

Throughout the world, poaching has been an ever-present threat to a vast array of species for over many decades. Traditional anti-poaching initiatives target catching the poachers. However, the challenge is far more complicated than catching individual poachers. Poaching is an industry which needs to be fully investigated. Many stakeholders are directly and indirectly involved in poaching activities (e.g., some local restaurants illegally providing meat to tourists). Therefore, stopping or severely decapitating the poaching industry requires a unified understanding of all stakeholders. The best way to uncover these geographical and social relationships is to track the movements of poachers. However, location tracking is challenging in most rural areas where wildlife sanctuaries are typically located. Internet-connected communication (e.g. 3G) technologies typically used in urban cities are not feasible in these rural areas. Therefore, we decided to develop an SMS (short message service) base low-cost tracking system (SMS-TRACCAR) to track poachers. The proposed system was developed to be deployed in Kinabatangan Wildlife Sanctuary, Sabah, Malaysia and nearby villages and cities where poachers typically move around. Our evaluations demonstrated that SMS-based tracking could provide sufficient quality (granular) data (with minimum energy consumption) that enable us to monitor poacher vehicle movements within rural areas where no other modern communication technologies are feasible to use. However, it is important to note that our system can be used in any domain that requires SMS-based geo-location tracking. SMS-TRACCAR can be configured to track individuals as well as groups. Therefore, SMS-TRACCAR contributes not only to the wildlife domain but in the wider context as well.Comment: Technical Repor

Simple rules for an efficient use of geographic information systems in molecular ecology

Geographic Information Systems (GIS) are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers publishing genomic data that is specifically suitable for landscape studies. GIS uniquely reveal the possibility to overlay genetic information with environmental data and, as such, allow us to locate and analyze genetic boundaries of various plant and animal species or to study gene-environment associations (GEA). This means that, using GIS, we can potentially identify the genetic bases of species adaptation to particular geographic conditions or to climate change. However, many biologists are not familiar with the use of GIS and underlying concepts and thus experience difficulties in finding relevant information and instructions on how to use them. In this paper, we illustrate the power of free and open source GIS approaches and provide essential information for their successful application in molecular ecology. First, we introduce key concepts related to GIS that are too often overlooked in the literature, for example coordinate systems, GPS accuracy and scale. We then provide an overview of the most employed open-source GIS-related software, file formats and refer to major environmental databases. We also reconsider sampling strategies as high costs of Next Generation Sequencing (NGS) data currently diminish the number of samples that can be sequenced per location. Thereafter, we detail methods of data exploration and spatial statistics suited for the analysis of large genetic datasets. Finally, we provide suggestions to properly edit maps and to make them as comprehensive as possible, either manually or trough programming languages

FOO: An upper-level ontology for the Forest Observatory

Wildlife and preservation research activities in the tropical forest of Sabah, Malaysia, can generate a wide variety of data. However, each research activity manages its data independently. Since these data are disparate, gaining unified access to them remains a challenge. We propose the Forest Observatory Ontology (FOO) as a basis for integrating different datasets. FOO comprises a novel upper-level ontology that integrates wildlife data generated by sensors. We used existing ontological resources from various domains (i.e., wildlife) to model FOO’s concepts and establish their relationships. FOO was then populated with multiple semantically modelled datasets. FOO structure and utility are subsequently evaluated using specialised software and task-based methods. The evaluation results demonstrate that FOO can be used to answer complex use-case questions promptly and correctly

The critical role of natural forest as refugium for generalist species in oil palm-dominated landscapes

In Borneo, oil palm plantations have replaced much of natural resources, where generalist species tend to be the principal beneficiaries, due to the abundant food provided by oil palm plantations. Here, we analyse the distribution of the Asian water monitor lizard (Varanus salvator) population within an oil palm-dominated landscape in the Kinabatangan floodplain, Malaysian Borneo. By using mark-recapture methods we estimated its population size, survival, and growth in forest and plantation habitats. We compared body measurements (i.e. body weight and body length) of individuals living in forest and oil palm habitats as proxy for the population’s health status, and used general least squares estimation models to evaluate its response to highly fragmented landscapes in the absence of intensive hunting pressures. Contrary to previous studies, the abundance of lizards was higher in the forest than in oil palm plantations. Recruitment rates were also higher in the forest, suggesting that these areas may function as a source of new individuals into the landscape. While there were no morphometric differences among plantation sites, we found significant differences among forested areas, where larger lizards were found inhabiting forest adjacent to oil palm plantations. Although abundant in food resources, the limited availability of refugia in oil palm plantations may intensify intra-specific encounters and competition, altering the body size distribution in plantation populations, contrary to what happens in the forest. We conclude that large patches of forest, around and within oil palm plantations, are essential for the dynamics of the monitor lizard population in the Kinabatangan floodplain, as well as a potential source of individuals to the landscape. We recommend assessing this effect in other generalist species, as well as the impact on the prey communities, especially to reinforce the establishment of buffer zones and corridors as a conservation strategy within plantations

Demography and rapid local adaptation shape Creole cattle genome diversity in the tropics

The introduction of Iberian cattle in the Americas after Columbus’ arrival imposed high selection pressures on a limited number of animals over a brief period of time. Knowledge of the genomic regions selected during this process may help in enhancing climatic resilience and sustainable animal production. We first determined taurine and indicine contributions to the genomic structure of modern Creole cattle. Second, we inferred their demographic history using approximate Bayesian computation (ABC), linkage disequilibrium (LD), and Ne Slope (NeS) analysis. Third, we performed whole genome scans for selection signatures based on cross‐population extended haplotype homozygosity (XP‐EHH) and population differentiation (FST) to disentangle the genetic mechanisms involved in adaptation and phenotypic change by a rapid and major environmental transition. To tackle these questions, we combined SNP array data (~54,000 SNPs) in Creole breeds with their modern putative Iberian ancestors. Reconstruction of the population history of Creoles from the end of the 15th century indicated a major demographic expansion until the introduction of zebu and commercial breeds into the Americas ~180 years ago, coinciding with a drastic Ne contraction. NeS analysis provided insights into short‐term complexity in population change and depicted a decrease/expansion episode at the end of the ABC‐inferred expansion, as well as several additional fluctuations in Ne with the attainment of the current small Ne only towards the end of the 20th century. Selection signatures for tropical adaptation pinpointed the thermoregulatory slick hair coat region, identifying a new candidate gene (GDNF), as well as novel candidate regions involved in immune function, behavioural processes, iron metabolism and adaptation to new feeding conditions. The outcomes from this study will help in future‐proofing farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance, resilience and welfare under climate change

Open data observatories: a survey

Open Data Observatories refer to online data platforms that provide free, real-time and historical data. They facilitate collaborative and unified environments for citizens and applications, supplemented with reusable datasets, analysis tools and interactive visualisations. Open Data Observatories collect and integrate various data types from multiple disparate providers. Data types include variables such as weather, traffic and social media, while providers are mainly the interconnected devices, services and individuals in the Internet of Things (IoT). The continually increasing volume and variety of such data require timely integration, management and analysis - yet to be presented in a way that end-users can easily understand. Data that interact in real-time preserve their value and enable a more in-depth understanding of real-world choices. This survey explored Open Data and reviewed twelve data observatories, focusing on their data management approaches. We investigated the observatories aims, designs and data types for some applied domains- namely transport, energy, environment, and social sensing. In what follows, we outlined five research challenges that influence their implementation