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62 results for “Migratory species”
Quantifying thermal exposure for migratory riverine species: phenology of Chinook salmon populations predicts thermal stress
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Structural and socioeconomic features of cities predict migratory bird species richness
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Seasonal density-dependence can select for partial migrants in migratory species
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Data from: Factors influencing plasticity in the arrival-breeding interval in a migratory species reacting to climate change
Climate change is profoundly affecting the phenology of many species. In migratory birds, there is evidence for advances in their arrival time at the breeding ground and their timing of breeding, yet empirical studies examining the interdependence between arrival and breeding time are lacking. Hence, evidence is scarce regarding how breeding time may be adjusted via the arrival-breeding interval to help local populations adapt to local conditions or climate change. We used long-term data from an intensively monitored population of the northern wheatear (Oenanthe oenanthe) to examine the factors related to the length of 734 separate arrival-to-breeding events from 549 individual females. From 1993 to 2017 the mean arrival and egg-laying dates advanced by approximately the same amount (~5-6 days), with considerable between-individual variation in the arrival-breeding interval. The arrival-breeding interval was shorter for: (1) individuals that arrived later in the season compared to early arriving birds, (2) for experienced females compared to first-year breeders, (3) as spring progressed, and (4) in later years compared to earlier ones. The influence of these factors was much larger for birds arriving earlier in the season compared to later arriving birds, with most effects on variation in the arrival-breeding interval being absent in late arriving birds. Thus, in this population it appears that the timing of breeding is not constrained by arrival for early- to mid-arriving birds, but instead is dependent on local conditions after arrival. For late arriving birds, however, the timing of breeding appears to be influenced by arrival constraints. Hence, impacts of climate change on arrival dates and local conditions are expected to vary for different parts of the population, with potential negative impacts associated with these factors likely to differ for early- versus late-arriving birds.
Data from: Tracking ice phenology by migratory waterbirds: settling phenology and breeding success of species with divergent population trends
<p>Dependence on climate-driven environmental cues in the initiation of life cycle stages is a critical attribute when assessing vulnerability of species to climate change impacts. This study focused on spring ice phenology as a cue to the settling of migratory waterbirds, asking whether there is an asynchrony between ice phenology and setting phenology that could affect breeding success of six species with divergent population trends. In the 37 study lakes in southeastern Finland, the ice-out date not only varied considerably between years, but became progressively earlier during the study period, 1991–2018. Settling phenology of all species tracked inter-annual variation in ice phenology. However, the degree of asynchrony between ice phenology and settling phenology varied between species, allowing discrimination between early and late settlers. Considerable inter-annual variation also occurred within species, but in only one species did the degree of asynchrony correlate with the ice-out date: for the horned grebe Podiceps auritus an earlier ice-out date meant greater asynchrony between settling phenology and ice phenology. The degree of asynchrony between settling phenology and ice phenology did not affect breeding success in any species. However, ice phenology per se affected breeding success of horned grebes: earlier ice-out was associated with lower annual breeding success. Breeding numbers of horned grebe showed a long-term decline. Results suggest that short-distance migratory birds are able to respond to climate change-driven phenological changes in their breeding environments, and that this ability may not depend on the relative timing of breeding.</p>
Data from: Genetic variation and seasonal migratory connectivity in Wilson's warblers (Wilsonia pusilla): species-level differences in nuclear DNA between western and eastern populations
There is growing interest in understanding patterns of seasonal migratory connectivity between breeding and wintering sites, both because differences in migratory behavior can be associated with population differentiation and because knowledge of migratory connectivity is essential for understanding the ecology, evolution, and conservation of migratory species. We present the first broad survey of geographic variation in the nuclear genome of breeding and wintering Wilson's warblers (Wilsonia pusilla), which have previously served as a research system for the study of whether genetic markers and isotopes can reveal patterns of migratory connectivity. Using 153 samples surveyed at up to 257 variable amplified fragment length polymorphism (AFLP) markers, we show that Wilson's warblers consist of highly distinct western and eastern breeding groups, with all winter samples grouping with the western breeding group. Within the west there is weak geographic differentiation, at a level insufficient for use in assignment of wintering samples to specific areas. The distinctiveness of western and eastern genetic groups, with no known intermediates, strongly suggests that these two groups are cryptic species. Analysis of mitochondrial cytochrome b sequence variation shows that the estimated coalescence time between western and eastern clades is roughly 2.3 million years ago, a surprisingly old time of divergence that is more typical of distinct species than of subspecies. Given their morphological similarity but strong genetic differences, western and eastern Wilson's warblers present a likely case of association between divergence in migratory behavior and the process of speciation.
Data from: Cryptic speciation and gene flow in a migratory songbird species complex: insights from the red-eyed vireo (Vireo olivaceus)
Migratory species that alternate between sympatry and allopatry over the course of an annual cycle are promising subjects for studies seeking to understand the process of speciation in the absence of strict geographic isolation. Here we sought to identify cryptic species and assess rates of gene flow in a clade of neotropical migrant songbirds in which geography and taxonomy are currently out of sync: the Red-Eyed Vireo (V. olivaceus) Species Complex. Phylogenetic, clustering, and statistical species delimitation analyses found that V. olivaceus includes two non-sister lineages migrating in opposite directions across the equator. Analyses of gene flow identified low levels of introgression between two species pairs, but none between northern and southern olivaceus. We also identified substantial well-supported conflicts between nuclear and mitochondrial topologies. Although the geographic distribution of mito-nuclear discordance is suggestive of hybridization and mitochondrial capture, we found no evidence of introgression in the nuclear genome of populations with discordant mitochondrial gene trees. Our study finds that species boundaries match breeding range and migratory phenology rather than the existing taxonomy in this group, and demonstrates the utility of genomic data in inferring species boundaries in recently diverged clades.
Data from: Using citizen science monitoring data in species distribution models to inform isotopic assignment of migratory connectivity in wetland birds
Stable isotopes have been used to estimate migratory connectivity in many species. Estimates are often greatly improved when coupled with species distribution models (SDMs), which temper estimates in relation to occurrence. SDMs can be constructed using from point locality data from a variety of sources including extensive monitoring data typically collected by citizen scientists. However, one potential issue with SDM is that these data oven have sampling bias. To avoid this potential bias, an approach using SDMs based on marsh bird monitoring program data collected by citizen scientists and other participants following protocols specifically designed to maximize detections of species of interest at locations representative of the species range. We then used the SDMs to refine isotopic assignments of breeding areas of autumn-migrating and wintering Sora (Porzana carolina), Virginia Rails (Rallus limicola), and Yellow Rails (Coturnicops noveboracensis) based on feathers collected from individuals caught at various locations in the United States from Minnesota south to Louisiana and South Carolina. Sora were assigned to an area that included much of the western U.S. and prairie Canada, covering parts of the Pacific, Central, and Mississippi Flyways. Yellow Rails were assigned to a broad area along Hudson and James Bay in northern Manitoba and Ontario, as well as smaller parts of Quebec, Minnesota, Wisconsin, and Michigan, including parts of the Mississippi and Atlantic Flyways. Virginia Rails were from several discrete areas, including parts of Colorado, New Mexico, the central valley of California, and southern Saskatchewan and Manitoba in the Pacific and Central Flyways. Our study demonstrates extensive data from organized citizen science monitoring programs are especially useful for improving isotopic assignments of migratory connectivity in birds, which can ultimately lead to better informed management decisions and conservation actions.
Genotype data for: Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex
<p>Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (<em>Alosa alosa</em>) and the twaite shad (<em>Alosa fallax</em>). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species <em>A. alosa</em>, which disperses greater distances compared to the iteroparous species, <em>A. fallax</em>. Individuals caught at sea were assigned at the river level for <em>A. fallax</em> and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: <em>A. agone</em> in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species' populations and their hybridization should be carefully considered while implementing conservation programs.</p>
Data from: Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail
Stable hydrogen isotope (δD) methods for tracking animal movement are widely used yet often produce low resolution assignments. Incorporating prior knowledge of abundance, distribution or movement patterns can ameliorate this limitation, but data are lacking for most species. We demonstrate how observations reported by citizen scientists can be used to develop robust estimates of species distributions and to constrain δD assignments. We developed a Bayesian framework to refine isotopic estimates of migrant animal origins conditional on species distribution models constructed from citizen scientist observations. To illustrate this approach, we analysed the migratory connectivity of the Virginia rail Rallus limicola, a secretive and declining migratory game bird in North America. Citizen science observations enabled both estimation of sampling bias and construction of bias-corrected species distribution models. Conditioning δD assignments on these species distribution models yielded comparably high-resolution assignments. Most Virginia rails wintering across five Gulf Coast sites spent the previous summer near the Great Lakes, although a considerable minority originated from the Chesapeake Bay watershed or Prairie Pothole region of North Dakota. Conversely, the majority of migrating Virginia rails from a site in the Great Lakes most likely spent the previous winter on the Gulf Coast between Texas and Louisiana. Synthesis and applications. In this analysis, Virginia rail migratory connectivity does not fully correspond to the administrative flyways used to manage migratory birds. This example demonstrates that with the increasing availability of citizen science data to create species distribution models, our framework can produce high-resolution estimates of migratory connectivity for many animals, including cryptic species. Empirical evidence of links between seasonal habitats will help enable effective habitat management, hunting quotas and population monitoring and also highlight critical knowledge gaps.
Migration-tracking integrated phylogeography supports long-distance dispersal-driven divergence for a migratory bird species in the Japanese archipelago
<p>Previous phylogeographic studies of migratory bird species have not discriminated long-distance dispersal (LDD) from vicariant speciation in their diversification process. We conducted an integrative phylogeographic approach to test the LDD hypothesis, which predicts that a Japanese migratory bird subspecies diverged from a population in the coastal region of the East China Sea (CRECS) via LDD over the East China Sea (ECS). We used the Brown Shrike as a model species, and we conducted molecular phylogenetics, species distribution models (SDMs) and migration tracking. We assessed whether the LDD hypothesis is applicable to the divergence history of the Japanese subspecies of the Brown Shrike.</p> <p>The datasets include three zipped files, namely DataS1.zip, DataS2.zip, and DataS3.zip. See the READ ME (AOKI_et_al_2021_DATASET_README.txt) for how each of the folder and files contained in them can be used to reproduce our results.</p> <p>DataS1.zip inlcudes an xml file to conduct the BEAST analysis. Molecular data, which include nucleotide sequences obtained for cytochrome b (cytb), cytochrome oxidase c subunit I (COI), myoglobin intron-2 (MB) and transforming growth factor beta 2 intron-5 (TGFb2), have been all reposited to DDBJ international nucleotide sequence database, and accession numbers have been already given to them. Accession numbers are provided in the appendix attached to the main manuscript.</p> <p>DataS2.zip includes several data that are related to produce occurrence data of the Brown Shrike used in the analysis and an R code to reproduce the SDMs. Explanatory climatic variables are all available at WorldClim v.1.4 (Hijmans et al., 2005), which are processed in the R code.</p> <p>DataS3.zip includes migratory route analyses using light-level geolocator data are available as the original light-level data and R codes. Sensitivity analyses were also conducted in these analyses, but their codes and results are seperately provided here.</p>
Use of amino acid isotope analysis to investigate capital versus income breeding strategies in migratory avian species
<p>Income and capital breeding represent opposing ends of a continuum of reproductive strategies. Quantifying nutrient allocation to reproduction is challenging, but recent advances in compound-specific stable isotope analysis hold promise for tracing the source of individual compounds allocated to reproduction. </p> <p>Here, we describe a novel approach of using measured carbon (δ<sup>13</sup>C) and nitrogen (δ<sup>15</sup>N) isotope values of individual amino acids (AAs) in pectoral muscle of egg-laying females and egg yolk as a useful tool to quantify the reliance on income versus capital breeding in migrating species. We used white-fronted (<em>Anser albifrons frontalis</em>), lesser snow (<em>A. caerulescens caerulescens</em>), and black brant (<em>Branta bernicla nigricans</em>) geese breeding in tundra ecosystems of northern Alaska as model organisms.</p> <p>All three species relied on mixed capital-income breeding strategies, but models based on AA isotope data estimated higher proportional contributions of endogenous resources to yolk synthesis compared to results based on bulk tissue isotope analyses. </p> <p>Tracing income versus capital nutrient allocation in migratory species at the compound level is a major advance from the current 'elemental' perspective obtained from bulk tissue stable isotope analyses. Our framework is applicable to all taxonomic groups, as long as there is a sufficient spatial or temporal isotopic gradient between resources obtained during the breeding and non-breeding periods.</p>
Data from: Breeding phenological response to spring weather conditions in common Finnish birds: resident species respond stronger than migratory species
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Data from: Climate change and nest predation affect shifts in timing and duration of breeding as well as reproductive success in a migratory species
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Data from: Factors influencing plasticity in the arrival-breeding interval in a migratory species reacting to climate change
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Seasonal distributions and predicting migratory pathways for three species of bats
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Data from: Genome-wide SNPs resolve spatiotemporal patterns of connectivity within striped marlin (Kajikia audax), a broadly distributed and highly migratory pelagic species
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Data from: Cryptic speciation and gene flow in a migratory songbird species complex: insights from the red-eyed vireo (Vireo olivaceus)
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Data from: Tracking ice phenology by migratory waterbirds: settling phenology and breeding success of species with divergent population trends
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Migration-tracking integrated phylogeography supports long-distance dispersal-driven divergence for a migratory bird species in the Japanese archipelago
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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.