Find research datasets worth reusing

opencc-by-4.0Dec 2019View details →

Data for: Does migration distance influence intra-individual variation in migratory behaviour in a seabird species with diverse migration strategies?

GPS tracking data from adult lesser black-backed gulls (L. fuscus) with 2 – 7 years of tracking data per individual from several colonies in the Netherlands, Belgium and the UK. This data has gone through initial cleaning to remove faulty GPS locations was combined with meta data from colonies to create a single .RDS file.  Result for the manuscript "High repeatability in migratory behaviours in a generalist seabird regardless of migration strategy" can be obtained from this data using the R scripts at https://github.com/jbrow247/LBBG_MigrationPlasticity_Pub.

opencc-by-4.0Mar 2020View details →

DATA SET FOR: Active faulting, submarine surface rupture and seismic migration along the Liquiñe-Ofqui fault system, Patagonian Andes

Data description: These data corresponde to high-resolution bathymetry and seismic reflection profiles obtained in the inner fjord west of Puerto Aysén (between 73.13°- 72.68°W and 45.32°-45.47°S; Figs. 1 and 2). The data set was obtained during a geophysical study as part of the DETSUFA project (Deslizamientos Tsunamigénicos en el Fiordo de Aysén; Lastras et al., 2013), which took place between March 4th  and 17th, 2013, aboard the R/V BIO Hésperides. KONGSBERG SIMRAD multibeam EM-1002S was used to obtain bathymetric data, and it works with 111 beams at a 96 kHz sonar frequency and with a maximum ping rate of >10 Hz. Equidistant mode was used for swath bathymetry acquisition. This array maximized the number of beams facilitating data acquisition and obtaining a homogenized final grid with improved resolution, with tracks separated every 150 m. The swath thickness was the same regardless of width, generating a 50% overlap between each track, with the exception of areas located near the coast. Expendable Bathythermograph (XBT) probes were used at specific sites to measure changes in water sound velocity due to eventual changes in fresh water circulation, tides, and sediment. Seismic reflection data were acquired using an array of two BOLT air guns (165 and 175 inches3), which were towed behind the vessel stern. The configuration used in the seismic sources was 2,000 psi, a depth of 3 m for the gun, with a firing rate of 15 m over the seafloor. A 100 m long mini-streamer with a 25 m active section, corresponding to one single channel, recovered the shots. The seismic data were recorded by using the DELPH SEISMICPLUS system with a recording length of 4.0 s and a preamplifier gain of 8 Hz. The raw seismic data were processed aboard the SMT Kingdom Suite, including the navigation and standard processes of electrical noise removing (50 Hz filter), gain amplifier and bandpass filtering, to improve data visualization.  Postprocessing  included  the  migration  of  the  sea  bottom  diffractions  and  the muting of the water column performed in Seismic-Unix. Files: Raw Seismic reflection data for lines 05, 06 and 07 (SU & SEG files) Masked Seismic profiles for lines 05, 06 and 07 (SU, PDF & PS files) Bathymetry of inner and outer Aysén Fjord (ASCII file)

Data from: Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes

While theory predicts that dispersal is a pivotal influence on speciation and extinction rates, it can have contradictory effects on each, such that empirical studies are needed to quantify its role. In many studies, dispersal reduction appears to promote diversification, although some analyses of migratory species suggest otherwise. Here we test for a relationship between migratory status and diversification rate within the dominant radiation of temperate Southern Hemisphere freshwater fishes, the Galaxiidae. We reconstructed a molecular phylogeny for the group, comprising >95% of extant lineages, and applied State-dependent Speciation Extinction models to estimate speciation, extinction, and diversification rates. In contrast to some previous studies, we revealed higher diversification rates in non-migratory lineages. The reduced gene flow experienced by non-migratory galaxiids appears to have increased diversification under conditions of allopatry or local adaptation. Migratory galaxiid lineages, by contrast, are genetically homogeneous within landmasses, but may also be rarely able to colonise other landmasses in the temperate Southern Hemisphere. The life history state exhibiting higher diversification likely reflects the spatial context of the study system relative to species dispersal abilities, by means of the intermediate dispersal model; the accurate quantification of dispersal abilities will aid in our understanding of these likely interactions.

opencc-zeroJun 2020View details →

Data from: Hurricanes overcome migration lag and shape intraspecific genetic variation beyond a poleward mangrove range limit

Expansion of many tree species lags behind climate-change projections. Extreme storms can rapidly overcome this lag, especially for coastal species, but how will storm-driven expansion shape intraspecific genetic variation? Do storms provide recruits only from the nearest sources, or from more distant sources? Answers to these questions have ecological and evolutionary implications, but empirical evidence is absent from the literature. Hurricane Irma provided an opportunity to address this knowledge gap at the northern range limit of the neotropical black mangrove (Avicennia germinans) on the Atlantic coast of Florida, USA. We observed massive post-hurricane increases in beach-stranded A. germinans propagules at, and past, this species' present-day range margin when compared to a previously-surveyed, non-hurricane year. Yet, propagule dispersal does not guarantee subsequent establishment and reproductive success (i.e., effective dispersal). We also evaluated prior effective dispersal along this coastline with isolated A. germinans trees identified beyond the most northern established population. We used 12 nuclear microsatellite loci to genotype hurricane-driven drift propagules from nine sites (n = 896 propagules) and isolated trees from four sites (n = 10 trees), determined their sources of origin, and estimated dispersal distances. Almost all drift propagules and all isolated trees came from the nearest sources. This research suggests that hurricanes are a prerequisite for poleward range expansion of a coastal tree species and that storms can shape the expanding gene pool by providing almost exclusively range-margin genotypes. These insights and empirical estimates of hurricane-driven dispersal distances should improve our ability to forecast distributional shifts of coastal species.

Data from: Among-individual and within-individual variation in seasonal migration covaries with subsequent reproductive success in a partially-migratory bird

Within-individual and among-individual variation in expression of key environmentally-sensitive traits, and associated variation in fitness components occurring within and between years, determine the extents of phenotypic plasticity and selection and shape population responses to changing environments. Reversible seasonal migration is one key trait that directly mediates spatial escape from seasonally-deteriorating environments, causing spatio-seasonal population dynamics. Yet, within-individual and among-individual variation in seasonal migration versus year-round residence, and dynamic associations with subsequent reproductive success, have not been fully quantified. We used novel capture-mark-recapture mixture models to assign individual European shags (Phalacrocorax aristotelis) to 'resident, 'early migrant' or 'late migrant' strategies in two consecutive years, using year-round local resightings. We demonstrate substantial among-individual variation in strategy within years, and directional within-individual change between years. Further, subsequent reproductive success varied substantially among strategies, and relationships differed between years; residents and late migrants had highest success in the two years respectively, matching the years in which these strategies were most frequently expressed. These results imply that migratory strategies can experience fluctuating reproductive selection, and that flexible expression of migration can be partially aligned with reproductive outcomes. Plastic seasonal migration could then potentially contribute to adaptive population responses to currently changing forms of environmental seasonality.

opencc-zeroNov 2019View details →

Data from: Migrating bison engineer the green wave

Newly emerging plants provide the best forage for herbivores. To exploit this fleeting resource, migrating herbivores align their movements to surf the wave of spring green-up. With new technology to track migrating animals, the Green Wave Hypothesis has steadily gained empirical support across a diversity of migratory taxa. This hypothesis assumes the green wave is controlled by variation in climate, weather, and topography, and its progression dictates the timing, pace, and extent of migrations. However, aggregate grazers that are also capable of engineering grassland ecosystems make some of the world's most impressive migrations, and it is unclear how the green wave determines their movements. Here we show that Yellowstone's bison (Bison bison) do not choreograph their migratory movements to the wave of spring green-up. Instead, bison modify the green wave as they migrate and graze. While most bison surfed during early spring, they eventually slowed and let the green wave pass them by. However, small-scale experiments indicated that feedback from grazing sustained forage quality. Most importantly, a 6-fold decadal shift in bison density revealed that intense grazing caused grasslands to green up faster, more intensely, and for a longer duration. Our finding broadens our understanding of the ways in which animal movements underpin the foraging benefit of migration. The widely accepted Green Wave Hypothesis needs to be revised to include large aggregate grazers that not only move to find forage, but also engineer plant phenology through grazing, thereby shaping their own migratory movements.

Data from: Genetic growth potential, rather than phenotypic size, predicts migration phenotype in Atlantic salmon

Knowledge of the relative importance of genetic versus environmental determinants of major developmental transitions is pertinent to understanding phenotypic evolution. In salmonid fishes, a major developmental transition enables a risky seaward migration that provides access to feed resources. In Atlantic salmon, initiation of the migrant phenotype, and thus age of migrants, is presumably controlled via thresholds of a quantitative liability, approximated by body size expressed long before the migration. However, how well size approximates liability, both genetically and environmentally, remains uncertain. We studied 32 Atlantic salmon families in two temperatures and feeding regimes (fully fed, temporarily restricted) to completion of migration status at age 1 year. We detected a lower migrant probability in the cold (0.42) than the warm environment (0.76), but no effects of male maturation status or feed restriction. By contrast, body length in late summer predicted migrant probability and its control reduced migrant probability heritability by 50–70%. Furthermore, migrant probability and length showed high heritabilities and between-environment genetic correlations, and were phenotypically highly correlated with stronger genetic than environmental contributions. Altogether, quantitative estimates for the genetic and environmental effects predicting the migrant phenotype indicate, for a given temperature, a larger importance of genetic than environmental size effects.

Data from: Chemical defenses shift with the seasonal vertical migration of a Panamanian poison frog

Dendrobatid poison frogs sequester lipophilic alkaloids from their arthropod prey to use as a form of chemical defense. Some dendrobatid frogs seasonally migrate between the leaf litter of the forest floor in the dry season to the canopy in the wet season, which may yield differences in prey (arthropods) and therefore alkaloid availability over space and time. Here, we document a seasonal vertical migration of Andinobates fulguritus (the yellow-bellied poison frog) from ground to canopy between dry and wet seasons. We observed turnover in alkaloid composition between seasons and found that dry season frogs contained a lower relative quantity of alkaloids; however, there was no change in alkaloid richness between seasons. The 77 alkaloids of 13 structural classes identified in this population appear to be derived mostly from mites and ants, though the two most common alkaloids were mite derived. Our observed shifts in defensive profiles are consistent with well-documented turnover in mite and ant communities between seasons and vertical strata. As climate change is expected to lengthen and strengthen dry seasons in many tropical regions, our results suggest that arboreal poison frogs forced to the ground for longer periods of time may see a shift in the abundance of alkaloids, possibly decreasing their defensive potential. This study provides further predictions for the wide-reaching effects of climate change, even as nuanced as charismatic poison frogs losing their poisons.

opencc-zeroAug 2020View details →

Data from: Stopover refueling, movement, and departure decisions in the White-throated Sparrow: the influence of intrinsic and extrinsic factors during spring migration

1. Differential migration timing between sex or age classes are examples of how migratory movement strategies can differ among sub-groups within a population. However, in songbirds, evidence for intrinsic differences in en route migratory behavior is often mixed, suggesting that the local environmental context may play a role in accentuating or diminishing patterns. 2. We evaluated how multiple intrinsic and extrinsic variables influenced refueling rates, local movement behavior, and departure decisions in the White-throated Sparrow (Zonotrichia albicollis) during spring migration. This species exhibits a unique genetically-based plumage dimorphism, providing a unique class of individual in which to evaluate patterns and processes of differential migration, in addition to sex, age, and migration distance. 3. At a migratory stopover site, plasma metabolite analysis was used to quantify individual variation in stopover refueling rate. In after second year adults, automated and manual radio telemetry was used to quantify daily activity timing, daily movement distances, stopover duration, and departure time. Arrival timing to the stopover site was determined using capture data. Non-breeding and previous breeding/natal latitude were determined using analysis of hydrogen isotopes in claws and feathers. 4. Males arrived at the stopover site 11 days on average before females, but no difference in migration timing was observed between plumage morph or age classes. After second year adults with more southern previous breeding latitudes arrived at stopover earlier whereas second year birds making their first return migration arrived at stopover in an inverse relationship to non-breeding latitude. Stopover refueling rate did not differ between ages, sexes, or plumage morphs, and daily departure probability of adults was higher under warmer temperatures and favorable tailwinds. White-striped morphs moved greater distances during stopover, initiated daily activity earlier in the morning, and departed for migration earlier in the evening than tan-striped morphs. 5. Our results show that while individual phenotype can influence some aspects of local stopover-scale movement behavior, evidence for differential stopover behavior was weak. Differential migration timing is unlikely to result from intrinsic differences in en route refueling rate and departure decisions, especially because the latter is strongly influenced by meteorological conditions.

opencc-by-4.0Sep 2020View details →

Logger data for article "Effects of blood parasite infections on spatiotemporal migration patterns and activity budgets in a long-distance migratory passerine"

The supplement loggerDATA.zip is a ZIP Archive (to be unzipped e.g. with <a href="https://www.izarc.org/downloads">https://www.izarc.org/downloads</a>) containing 40 folders and one .txt file. In the readME.txt file one can find a detailed description of the folder content and the data specifications of the files used for the analyses in the article "Effects of blood parasite infections on spatiotemporal migration patterns and activity budgets in a long-distance migratory passerine". For more information of how the data can be analysed and visualised please see: <a href="https://kiranlda.github.io/PAMLrManual/">https://kiranlda.github.io/PAMLrManual/</a>.

opencc-zeroSep 2020View details →

New insights into the patterns and drivers of avian altitudinal migration from a growing crowdsourcing data source

Altitudinal migration is a common and important but understudied behavior in birds. Difficulty in characterizing avian altitudinal migration has prevented a comprehensive understanding of this behavior. To address this, we investigated the altitudinal migration patterns and explored potential drivers for a major proportion (~70%) of the entire resident bird community along an almost 4,000 m elevational gradient on the main island of Taiwan. Based on the occurrence records collected by citizen scientists, we examined the seasonal shifts in the center and the upper and lower boundaries of elevational distributions for 104 individual species. We then built phylogeny-controlled regression models to investigate the associations between the birds' seasonal distribution shifts and seven of their traits, and examined whether the observed shifts can be explained by three main hypotheses on potential drivers. Results showed that at least 60 species (58%) seasonally changed their distributions along elevations. While most of them (42 species) tended to move downhill in winter, a considerable number of species (14) tended to move uphill. While the species breeding at high or low elevations tended to move downhill in winter, those breeding at medium-low elevations tended to move or extend their distributions to higher elevations. Our regression models suggested that seasonal variations in climates and food availability could be major drivers of the behavior. However, the three hypotheses can only partially explain the observed downhill migration patterns and none of them can well explain the uphill patterns, indicating an important knowledge gap. This study investigated avian altitudinal migration from a new perspective with a novel and generalizable approach, and revealed interesting patterns that could be difficult to identify with conventional approaches. It demonstrated the power of citizen science data to provide new insights into this behavior by characterizing the general patterns and mechanisms across a large number of species.

openmit-licenseSep 2020View details →

Analysis of migration patterns of western marsh harriers using GPS tracking data

This repository contains analysis code for Vansteelant et al. (2020, <a href="https://doi.org/10.1007/s10336-020-01785-6">https://doi.org/10.1007/s10336-020-01785-6</a>). See the <code>README.md</code> for more information.

opencc-by-4.0Sep 2020View details →

Migration variables and infection data for article "Effects of blood parasite infections on spatiotemporal migration patterns and activity budgets in a long-distance migratory passerine"

Data related to the article "Effects of blood parasite infections on spatiotemporal migration patterns and activity budgets in a long-distance migratory passerine" in the format .csv. The 1st file (SupplTab_EcoEvo_data.csv) contains all variables used for the analyses and the 2nd file (SupplTab_EcoEvo_glossary.csv) contains explanations about the variables in the 1st file.

opencc-by-4.0Dec 2020View details →

Fiji/CellProfiler cell migration timelapse data set and code

This zenodo upload consists of: Fiji IJMacro script create_LabelledMasks.ijm CellProfiler pipeline TrackMate_CellProfiler.cppipe Matlab script Plot_per_cell.m  Saved manually curated TrackMate project crop_1_60_ManualCuration.xml Saved Spots Results Table of manually curated TrackMate project: Spots in tracks statistics.csv CellProfiler pipeline output cp_output.zip Example data set crop_1_60.tif - subset of image data previously described in: <a href="https://www.zotero.org/google-docs/?9YEDuq">Shafqat-Abbasi, H., Kowalewski, J. M., Kiss, A., Gong, X., Hernandez-Varas, P., Berge, U., Jafari-Mamaghani, M., Lock, J. G., and Strömblad, S. 2016. An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes. eLife 5:e11384–e11384.</a> Many thanks to Staffan Strömblad et al. for sharing the data.

opencc-zeroDec 2017View details →

Data from: Sora (Porzana carolina) autumn migration habitat use

Palustrine wetland management across the United States is often conducted under a moist soil management framework aimed at providing energetic resources for non-breeding waterfowl. Moist soil management techniques typically include seasonal water-level manipulations and mechanical soil disturbance to create conditions conducive to germination and growth of early successional, seed-producing wetland plants. The assumption is that providing stopover and wintering habitat for non-breeding waterfowl will also accommodate life history needs of a broader suite of migratory waterbirds including shorebirds, wading birds, and marsh birds. Although studies of wetlands provide some evidence to support this assumption for shorebirds and wading birds, there is less information on how other marshbirds, respond. Sora (Porzana carolina) are a species of migratory rail that depends on wetlands year round as it migrates across North America. It is a species for which the consequences of wetland management decisions directed toward non-breeding waterfowl, is unknown. We conducted nocturnal surveys on 10 public properties in Missouri, USA during autumn migration from 2012-2016 to examine Sora habitat use in wetland impoundments managed to enhance production of moist soil vegetation. We found a positive relationship with Sora presence and mean water depth and annual moist soil vegetation; Sora used, on average, deeper water than was available across surveyed impoundments and used locations with a higher percentage of annual moist soil vegetation than was available. We found a negative relationship with Sora use and upland vegetation, woody vegetation, and open water. We found Sora using deeper water than have previously been reported for autumn migration and that moist soil management techniques used on Missouri's intensively-managed public wetland areas may be compatible with Sora autumn migration stopover habitat requirements.