ALBERT

Description: Our understanding of mammal ecology has always been hindered by the difficulties of observing species in closed tropical forests. Camera trapping has become a major advance for monitoring terrestrial mammals in biodiversity rich ecosystems. Here we compiled one of the largest datasets of inventories of terrestrial mammal communities for the Neotropical region based on camera trapping studies. The dataset comprises 170 surveys of medium to large terrestrial mammals using camera traps conducted in 144 areas by 74 studies, covering six vegetation types of tropical and subtropical Atlantic Forest of South America (Brazil and Argentina), and present data on species composition and richness. The complete dataset comprises 53,438 independent records of 83 species of mammals, includes 10 species of marsupials, 15 rodents, 20 carnivores, 8 ungulates and 6 armadillos. Species richness averaged 13 species (± 6.07 SD) per site. Only six species occurred in more than 50% of the sites: the domestic dog Canis familiaris , crab-eating fox Cerdocyon thous , tayra Eira barbara , south American coati Nasua nasua , crab-eating raccoon Procyon cancrivorus and the nine-banded armadillo Dasypus novemcinctus . The information contained in this dataset can be used to understand macroecological patterns of biodiversity, community, and population structure, but also to evaluate the ecological consequences of fragmentation, defaunation, and trophic interactions. This article is protected by copyright. All rights reserved.

Description: Herein, we use genetic data from 277 sleeper sharks to perform coalescent-based modeling to test the hypothesis of early Quaternary emergence of the Greenland shark ( Somniosus microcephalus ) from ancestral sleeper sharks in the Canadian Arctic-Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus pacificus can be genetically distinguished using combined mitochondrial and nuclear DNA markers. Our data confirm the presence of genetically admixed individuals in the Canadian Arctic and sub-Arctic, and temperate Eastern Atlantic regions, suggesting introgressive hybridization upon secondary contact following the initial species divergence. Conservative substitution rates fitted to an Isolation with Migration (IM) model indicate a likely species divergence time of 2.34 Ma, using the mitochondrial sequence DNA, which in conjunction with the geographic distribution of admixtures and Pacific signatures likely indicates speciation associated with processes other than the closing of the Isthmus of Panama. This time span coincides with further planetary cooling in the early Quaternary period followed by the onset of oscillating glacial-interglacial cycles. We propose that the initial S. microcephalus – S. pacificus split, and subsequent hybridization events, were likely associated with the onset of Pleistocene glacial oscillations, whereby fluctuating sea levels constrained connectivity among Arctic oceanic basins, Arctic marginal seas, and the North Atlantic Ocean. Our data demonstrates support for the evolutionary consequences of oscillatory vicariance via transient oceanic isolation with subsequent secondary contact associated with fluctuating sea levels throughout the Quaternary period—which may serve as a model for the origins of Arctic marine fauna on a broad taxonomic scale. Using genetic data, we perform coalescent-based modeling to test the hypothesis of the early Quaternary emergence of the Greenland shark ( Somniosus microcephalus ) from ancestral sleeper sharks in the Canadian Arctic-Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus pacificus can be genetically distinguished using combined mitochondrial and nuclear DNA markers. We demonstrate support for the evolutionary consequences of oscillatory vicariance with secondary contact in via transient oceanic isolation associated with fluctuating sea levels during the late Miocene and Quaternary periods—which may serve as a model for origins of Arctic and Antarctic marine fauna on a broad taxonomic scale.

Description: Widespread ocean acidification (OA) is modifying the chemistry of the global ocean, and the Arctic is recognised as the region where the changes will progress at the fastest rate. Moreover, Arctic species show lower capacity for cellular homeostasis and acid-base regulation rendering them particularly vulnerable to OA. In the present study, we found physiological differences in OA response across geographically separated populations of the keystone Arctic copepod Calanus glacialis . In copepodite stage CIV, measured reaction norms of ingestion rate and metabolic rate showed severe reductions in ingestion and increased metabolic expenses in two populations from Svalbard (Kongsfjord and Billefjord) whereas no effects were observed in a population from the Disko Bay, West Greenland. At pH T 7.87, which has been predicted for the Svalbard west coast by year 2100, these changes resulted in reductions in scope for growth of 19% in the Kongsfjord and a staggering 50% in the Billefjord. Interestingly, these effects were not observed in stage CV copepodites from any of the three locations. It seems that CVs may be more tolerant to OA perhaps due to a general physiological reorganisation to meet low intracellular pH during hibernation. Needless to say, the observed changes in the CIV stage will have serious implications for the C. glacialis population health status and growth around Svalbard. However, OA tolerant populations such as the one in the Disko Bay could help to alleviate severe effects in C. glacialis as a species. This article is protected by copyright. All rights reserved.

Description: Radio frequency identification (RFID) provides a simple and inexpensive approach for examining the movements of tagged animals, which can provide information on species behavior and ecology, such as habitat/resource use and social interactions. In addition, tracking animal movements is appealing to naturalists, citizen scientists, and the general public and thus represents a tool for public engagement in science and science education. Although a useful tool, the large amount of data collected using RFID may quickly become overwhelming. Here, we present an R package ( feedr ) we have developed for loading, transforming, and visualizing time-stamped, georeferenced data, such as RFID data collected from static logger stations. Using our package, data can be transformed from raw RFID data to visits, presence (regular detections by a logger over time), movements between loggers, displacements, and activity patterns. In addition, we provide several conversion functions to allow users to format data for use in functions from other complementary R packages. Data can also be visualized through static or interactive maps or as animations over time. To increase accessibility, data can be transformed and visualized either through R directly, or through the companion site: http://animalnexus.ca , an online, user-friendly, R-based Shiny Web application. This system can be used by professional and citizen scientists alike to view and study animal movements. We have designed this package to be flexible and to be able to handle data collected from other stationary sources (e.g., hair traps, static very high frequency (VHF) telemetry loggers, observations of marked individuals in colonies or staging sites), and we hope this framework will become a meeting point for science, education, and community awareness of the movements of animals. We aim to inspire citizen engagement while simultaneously enabling robust scientific analysis. Although radio frequency identification (RFID) provides a simple and inexpensive approach for examining the movements of tagged animals, the large amount of data collected quickly becomes overwhelming. We present an R package, feedr , and its companion website, animalnexus.ca, which provide powerful, yet user-friendly tools for loading, transforming, and visualizing time-stamped, georeferenced data (such as RFID) collected from static logger stations.

Description: Luminescence dating of desert dune sediments has generated many hundreds of ages, many used in reconstructions of Quaternary environmental changes, others in attempts to elucidate dune processes. Environmental and climatic interpretations of these records have proved problematic and it remains challenging to test hypotheses of the systematic response of dunefields to changes in external forcing in the past and to make predictions of the future. We use a method that quantifies dune sediment accumulation to interpret dune luminescence age datasets, rather than simply using the ages themselves as proxies of change. The Accumulation Intensity method allows periods of dune sediment accumulation, here over the timescale 10 2 -10 5 years, to be identified from compilations of dated sand sea stratigraphic sequences. We apply this approach to two of the largest dune age datasets, from southern Africa and Australia, testing whether or not dunefield accumulation has co-varied in the Late Quaternary and whether systematic relationships to external drivers at global, hemispheric, regional and local scales can be identified.

Description: Groundwater resources of the Republic of the Maldives are threatened by a variety of factors including variable future rainfall patterns, continued population growth and associated pumping demands, rising sea level, and contamination from the land surface. This study assesses changes in groundwater availability due to variable rainfall patterns and sea level rise (SLR) in the coming decades, a key component of water resources management for the country. Using a suite of two-dimensional density-dependent groundwater flow models, time-dependent thickness of the freshwater lens is simulated for a range of island sizes (200 m to 1100 m) during the time period of 2011 to 2050, with recharge to the freshwater lens calculated using rainfall patterns provided by General Circulation Models (GCM) for the three distinct geographic regions of the Maldives. The effect of SLR on the freshwater lens is quantified using estimates of shoreline recession and associated decreases in island width. If rainfall is solely considered, groundwater availability is projected to increase, as lens thickness during the 2031-2050 time periods is slightly greater (1-5%) than during the 2011-2030 time period. However, including the impact of SLR indicates an overall decrease in lens thickness, with drastic decreases (60% to 100%) projected for small islands (200 m) and moderate decreases (12% to 14%) expected for 400 m islands, which accommodate one-third of the national population. Similar methodologies can be used for other atoll island nations, such as the Republic of Marshall Islands, Federated States of Micronesia and the Republic of Kiribati. For the Maldives, results from this study can be used in conjunction with population growth estimates to determine the feasibility of including groundwater in water resources planning and management for the country.

Description: We introduce a new representation of coupled solute and water- age dynamics at the catchment scale, which shows how the contributions of young runoff waters can be directly referenced to observed water-quality patterns. The methodology stems from recent trends in hydrologic transport that acknowledge the dynamic nature of streamflow age and explores the use of water age fractions as an alternative to the mean age. The approach uses a travel-time-based transport model to compute the fractions of streamflow that are younger than some thresholds (e.g. younger than a few weeks) and compares them to observed solute concentration patterns. The method is here validated with data from the Hubbard Brook Experimental Forest (HBEF) during spring 2008, where we show that the presence of water younger than roughly 2 weeks, tracked using a hydrologic transport model and deuterium measurements, mimics the variation in dissolved silicon concentrations. Our approach suggests that an age-discharge relationship can be coupled to classic concentration-discharge relationship, to identify the links between transport timescales and solute concentration. Our results highlight that the younger streamflow components can be crucial for determining water quality variations and for characterizing the dominant hydrologic transport dynamics.

Description: This paper describes a new data set from the Aeronomy of Ice in the Mesosphere (AIM) Cloud Imaging and Particle Size (CIPS) instrument, from which gravity waves (GWs) at an altitude of 50-55 km can be inferred. CIPS is sensitive to GWs with horizontal wavelengths from ~15-600 km and vertical wavelengths longer than 15 km. Several examples of GWs in CIPS observations are shown, including waves associated with the Andes mountains, island topography, convection, the polar night jet, and the tropospheric jet stream. GW signatures in the CIPS data are shown to agree well with near-coincident but lower-altitude measurements from the Atmospheric InfraRed Sounder (AIRS) in June of 2016. Results suggest the power of combining CIPS measurements with those from other instruments to investigate GW filtering and propagation. The CIPS data set opens new areas of inquiry, enabling comprehensive investigations of GWs in the middle atmosphere on a near-global scale.

Description: Emerging infectious diseases (EIDs) are a salient threat to many animal taxa, causing local and global extinctions, altering communities and ecosystem function. The EID chytridiomycosis is a prominent driver of amphibian declines, which is caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). To guide conservation policy, we developed a predictive decision-analytic model that combines empirical knowledge of host-pathogen metapopulation dynamics with expert judgment regarding effects of management actions, to select from potential conservation strategies. We apply our approach to a boreal toad ( Anaxyrus boreas boreas ) and Bd system, identifying optimal strategies that balance tradeoffs in maximizing toad population persistence and landscape-level distribution, while considering costs. The most robust strategy is expected to reduce the decline of toad breeding sites from 53% to 21% over 50 years. Our findings are incorporated into management policy to guide conservation planning. Our online modeling application provides a template for managers of other systems challenged by EIDs. This article is protected by copyright. All rights reserved

Description: Ocean acidification is the increase in seawater p CO 2 due to the uptake of atmospheric anthropogenic CO 2 , with the largest changes predicted to occur in the Arctic seas. For some marine organisms, this change in p CO 2 , and associated decrease in pH, represents a climate change-related stressor. In this study, we investigated the gene expression patterns of nauplii of the Arctic copepod Calanus glacialis cultured at low pH levels. We have previously shown that organismal-level performance (development, growth, respiration) of C. glacialis nauplii is unaffected by low pH. Here, we investigated the molecular-level response to lowered pH in order to elucidate the physiological processes involved in this tolerance. Nauplii from wild-caught C. glacialis were cultured at four pH levels (8.05, 7.9, 7.7, 7.5). At stage N6, mRNA was extracted and sequenced using RNA-seq. The physiological functionality of the proteins identified was categorized using Gene Ontology and KEGG pathways. We found that the expression of 151 contigs varied significantly with pH on a continuous scale (93% downregulated with decreasing pH). Gene set enrichment analysis revealed that, of the processes downregulated, many were components of the universal cellular stress response, including DNA repair, redox regulation, protein folding, and proteolysis. Sodium:proton antiporters were among the processes significantly upregulated, indicating that these ion pumps were involved in maintaining cellular pH homeostasis. C. glacialis significantly alters its gene expression at low pH, although they maintain normal larval development. Understanding what confers tolerance to some species will support our ability to predict the effects of future ocean acidification on marine organisms. We investigated the gene expression of the Arctic copepod Calanus glacialis nauplii cultured at low pH levels to elucidate the physiological processes involved in their acclimation to future ocean acidification (OA). We found significant changes in C. glacialis gene expression at low pH, including regulation of ion exchange activity, DNA transcription, molecular chaperones, locomotor activity, and stress response genes. A general downregulation of stress response genes may be a characteristic of tolerant species.