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Fig. 1 in Can north american fish passage tools work for South american migratory fishes?
Fig. 1. Comparison of observed and NFS predicted (based on 5,000 virtual fish) emigrant passage proportions for 23 configurations for behavior rules turned on (A) and behavior rules turned off (B) (virtual emigrants act as passive particles). Passage (exit) routes are bypass, spillway and turbines. Routes with either 0% or 100% of river flow in CFD model are not plotted or factored into trend lines. Sources of observed data are described in Goodwin et al. (2006).
Fig. 4 in Can north american fish passage tools work for South american migratory fishes?
Fig. 4. Comparison of 3-D tagged (left) and virtual (right) emigrant tracks for Lower Granite Dam 2003 RSW. Dam operation described in Goodwin et al. (2006). CFD model depiction of forebay hydrodynamic pattern in Fig. 5. Acoustic-tag emigrant track provided by U.S. Geological Survey (Cash et al., 2005).
Fig. 3 in Can north american fish passage tools work for South american migratory fishes?
Fig. 3. Project features at Lower Granite Dam on the Snake River, WA USA for 2000 and 2003 studies [A]. The Behavioral Guidance Structure (BGS) is intended to guide emigrants to the Surface Bypass Collector (SBC) and occlude them from the 3 turbine intakes nearest the shore. In 2003, a Removable Spillway Weir (RSW) was deployed in the spillbay nearest the powerhouse in lieu of the SBC; the BGS was also removed. Acoustic-tag emigrant track (green in [B]) provided by U.S. Geological Survey (Cash et al., 2002). CFD model depiction of forebay hydrodynamic pattern for [B], [C] and [D] in Fig. 5a.
Data from: Spatial consistency in drivers of population dynamics of a declining migratory bird
<p>1. Many migratory species are in decline across their geographical ranges. Single-population studies can provide important insights into drivers at a local scale, but effective conservation requires multi-population perspectives. This is challenging because relevant data are often hard to consolidate, and state-of-the-art analytical tools are typically tailored to specific datasets.</p> <p>2. We capitalized on a recent data harmonization initiative (SPI-Birds) and linked it to a generalized modeling framework to identify the demographic and environmental drivers of large-scale population decline in migratory pied flycatchers (<em>Ficedula</em> <em>hypoleuca</em>) breeding across Britain.</p> <p>3. We implemented a generalized integrated population model (IPM) to estimate age-specific vital rates, including their dependency on environmental conditions, and total and breeding population size of pied flycatchers using long-term (34–64 years) monitoring data from seven locations representative of the British breeding range. We then quantified the relative contributions of different vital rates and population structures to changes in short- and long-term population growth rates using transient life table response experiments (LTREs).</p> <p>4. Substantial covariation in population sizes across breeding locations suggested that change was the result of large-scale drivers. This was supported by LTRE analyses, which attributed past changes in short-term population growth rates and long-term population trends primarily to variation in annual survival and dispersal dynamics, which largely act during migration and/or non-breeding season. Contributions of variation in local reproductive parameters were small in comparison, despite sensitivity to local temperature and rainfall within the breeding period.</p> <p>5. We show that both short- and longer-term population changes of British-breeding pied flycatchers are likely linked to factors acting during migration and in non-breeding areas, where future research should be prioritized. We illustrate the potential of multi-population analyses for informing management at (inter)national scales and highlight the importance of data standardization, generalized and accessible analytical tools, and reproducible workflows to achieve them.</p>
Intermediate files accompanying manuscript "The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid".
<p>Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (<em>Oncorhynchus nerka</em>) exhibit migratory and resident (‘kokanee’) ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have a recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies, and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12, and 20, associated with migratory behaviour, spawning location, and spawning timing. Several structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (<em>SYNGAP</em>, <em>TPM3</em>), as well as eye and brain development (including <em>SIX6</em>), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (<em>GREB1L</em>, <em>ROCK1</em>) identified have been associated with timing of migration in other salmonids and could explain variation in timing of spawning in our study. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.</p>
Insights into natal origins of migratory Nearctic hover flies (Diptera: Syrphidae): New evidence from stable isotope (δ2H) assignment analyses
<p>Hover flies (Diptera: Syrphidae) are an important group of insects that provide a multitude of key ecosystem services including pollination and biological control, yet many of their major life history traits are not understood. Some Palearctic hover fly species are known to migrate in response to changing seasonal conditions, yet this behavior is almost entirely unrecognized in Nearctic species. At least one species, <em>Eupeodes</em> <em>americanus</em> (Wiedemann 1830), is partially migratory during autumn while <em>Allograpta</em> <em>obliqua</em> may be non-migratory, but it is unknown where these insects originate and how far they may travel. We examined natal origins of two Nearctic hover fly species, <em>Allograpta</em> <em>obliqua</em> and <em>Eupeodes</em> <em>americanus</em>, using stable hydrogen isotope (δ<sup>2</sup>H) measurements of metabolically inactive tissues (wings and legs) to derive a hover fly δ<sup>2</sup>H isoscape. While <em>Allograpta</em> <em>obliqua</em> was mostly of local origin, several <em>Eupeodes</em> <em>americanus</em> were sourced from northern latitudes in the Midwestern United States and Canada, representing travel distances of up to 3,000 km likely using seasonally favorable air currents. This phenomenon is expected to have major ecological and economic ramifications, especially in the realm of plant pollination ecology and biological control.</p>
Non-reproductive dispersal: An important driver of migratory range dynamics and connectivity
<p>Dispersal is the primary ecological process underpinning spatial dynamics in motile species by generating flux in reproductive locations over time. In migratory species, dispersal can also occur around non-breeding ranges, but this form currently lacks a unifying theoretical framework. We present a novel conceptual model for dispersal in migrants that builds upon existing literature, differentiating 'reproductive' dispersal (i.e. changes in breeding locations) from 'non-reproductive' dispersal, which we define as movements resulting in inter-annual or inter-generational changes in non-breeding locations. Crucially, unlike reproductive dispersal where movement outcomes are naturally propagated between generations, the outcomes of non-reproductive dispersal can be non-heritable even if dispersers survive to reproduce. We simulate a non-social migratory population with a genetically-determined migratory programme to model how heritability of this program influences both migratory connectivity and range shift propensity. When exposed to spatially-uncoupled shifts in habitable ranges (i.e. seasonal climate niches shifting at different rates), long-term persistence of simulated populations required changes in migratory programmes to arise through heritable forms of non-reproductive dispersal (e.g. mutations in migratory gene complexes). By contrast, non-heritable dispersal mechanisms (e.g. weather drift, navigation errors) did not drive long-term shifts in non-breeding ranges, despite being a major component of realised dispersal and migratory connectivity patterns. Migratory connectivity metrics conflate these heritable and non-heritable drivers of non-reproductive dispersal and therefore have limited power in predicting spatial population responses to environmental change. Our models provide a framework for improving our understanding of spatial dynamics in migratory populations and highlight the importance of teasing apart the genetic or cultural mechanisms that drive inter-generational migratory variability in order to evaluate and predict range plasticity in migrants.</p>
Data and code from: Three decades of wildlife-vehicle collisions in a protected area: main roads and long-distance commuting trips to migratory prey increase spotted hyena roadkills in the Serengeti
<p>This is the first release. Potential updates will be available on GitHub: <a href="https://github.com/MarwanNaciri/Three_decades_of_spotted_hyena_roadkill_in_a_protected_area">https://github.com/MarwanNaciri/Three_decades_of_spotted_hyena_roadkill_in_a_protected_area</a></p>
Data for: Early life conditions influence fledging success and subsequent local recruitment rates in a declining migratory songbird, the Whinchat Saxicola rubetra
<ol> <li>Life history traits and environmental conditions influence reproductive success in animals, and consequences of these can influence subsequent survival and recruitment into breeding populations. Understanding influences on demographic rates is required to determine the causes of decline. Migratory species experience spatially and temporally variable conditions across their annual cycle, making identifying where the factors influencing demographic rates operate challenging.</li> <li>Here, we use the Whinchat <em>Saxicola</em> <em>rubetra</em> as a model declining long-distance migrant bird. We analyse 10 years of data from 247 nesting attempts and 2519 post-fledging observations of 1193 uniquely marked nestlings to examine the influence of life history traits, habitat characteristics and weather on survival of young from the nestling stage to local recruitment into the natal population.</li> <li>We detected potential silver spoon effects where conditions during the breeding stage influence subsequent apparent local recruitment rates, with higher recruitment for fledglings from larger broods, and recruitment rate negatively related to rainfall that chicks experienced in-nest. Additionally, extreme temperatures experienced pre- and post-fledging increased fledging success and recruitment rate. However, we could not determine whether this was driven by temperature influencing mortality during the post-fledging period or later in the annual cycle.</li> <li>Brood size declined with hatching date. In-nest survival increased with brood size and was highest at local temperature extremes. Furthermore, nest survival was highest at nests surrounded with 40–60% vegetation cover of Bracken <em>Pteridium</em> <em>aquilinum</em> within 50m of the nest.</li> <li>Our results show that breeding phenology and environmental factors may influence fledging success and recruitment in songbird populations, with conditions experienced during the nestling stage influencing local recruitment rates in Whinchats (i.e. silver spoon effect). Recruitment rates are key drivers of songbird population dynamics. Our results help identify some of the likely breeding season mechanisms that could be important population drivers.</li> </ol>
Figure 3. A European Robin, Erithacus rubecula. A in Capturing migratory birds and examining for ticks (Acari: Ixodida)
Figure 3. A European Robin, Erithacus rubecula. A. Examination of tick presence, B. Collection of immature ticks by a tweezer.
Figure 2 in Capturing migratory birds and examining for ticks (Acari: Ixodida)
Figure 2. Willow Warbler, Phylloscopus trochilus, parasitized by a fully engorged nymph (Hyalomma sp.). A. Dorsal view, B. Lateral view.
Figure 1. A in Capturing migratory birds and examining for ticks (Acari: Ixodida)
Figure 1. A. Erected mist net in Cernek bird ringing station, B. Caught birds in mist net, C. A Garden Warbler, Sylvia borin, captured by mist net.
Manipulation of photoperiod induces fat storage, but not fat mobilization in the migratory songbird, Dumetella carolinensis (Gray Catbird) 1.
<p>Datasets for "Manipulation of photoperiod induces fat storage, but not fat mobilization in the migratory songbird, Dumetella carolinensis (Gray Catbird)" publication in the Journal of Comparative Physiology B.</p>
Predation risk drives long-term shifts in migratory behavior and demography in a large herbivore population
<p>Migration is an adaptive life-history strategy that helps individuals across taxa maximize fitness by obtaining forage and avoiding predation risk. The mechanisms driving migratory changes are poorly understood, and links between migratory behavior, space use, and demographic consequences are rare. Here, we use a nearly 20-year record of individual-based monitoring of elk (<em>Cervus canadensis</em>) to test hypotheses for changing patterns of migration in a large herbivore, elk (<em>Cervus canadensis</em>), in and adjacent to a large protected area in Banff National Park (BNP), Canada. We test whether bottom-up (forage quality) or top-down (predation risk) factors explained trends in i) the proportion of individuals using 5 different migratory tactics, ii) differences in survival rates of migratory tactics during migration and whilst on summer ranges, iii) cause-specific mortality by wolves and grizzly bears, and iv) population abundance. We found dramatic shifts in migration consistent with behavioral plasticity in individual choice of annual migratory routes. Shifts were inconsistent with exposure to the bottom-up benefits of migration. Instead, exposure to landscape gradients in predation risk caused by exploitation outside the protected area drove migratory shifts. Carnivore exploitation outside the protected area led to higher survival rates for female elk remaining resident or migrating outside the protected area. Cause-specific mortality aligned with exposure to predation risk along migratory routes and summer ranges. Wolf predation risk was higher on migratory routes than summer ranges of montane-migrant tactics, but wolf predation risk traded-off with heightened risk from grizzly bears on summer ranges. A novel eastern migrant tactic emerged following a large forest fire that enhanced forage in an area with lower predation risk outside of the protected area. The changes in migratory behavior translated to population abundance, where abundance of the montane-migratory tactics declined over time. The presence of diverse migratory life histories maintained a higher total population abundance than would have been the case with one migratory tactic in the population. Our study demonstrates the complex ways in which migratory populations change over time through behavioral plasticity and associated demographic consequences because of individuals balancing predation risk and forage trade-offs.</p>
Energetic trade-offs in migration decision-making, reproductive effort, and subsequent parental care in a long-distance migratory bird
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The role of tropical rainfall in driving range dynamics for a long-distance migratory bird
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Data from: Environmental drivers of population-level variation in the migratory and diving ontogeny of an Arctic top predator
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Data from: Migratory singers dynamically overlap the signal space of a breeding warbler community
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Route flexibility is associated with headwind minimization in a long-distance migratory seabird
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Fitness consequences of anthropogenic subsidies for a partially migratory wading bird
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ScienceDex guides
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.