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Songbird surveys , 1952 - 1964, 1983 - 2008 Adirondack Long-Term Ecological Monitoring Program Project No. 2 Breeding Birds by Adirondack Ecological Center of the State University of New York College of Environmental Science and Forestry, Newcomb, New York. Environmental Data Initiative.
Study objectives were to (1) Document long-term trends in relative abundance and diversity of breeding forest birds (songbirds) in forest stands with different harvest histories and (2) Identify bird species that can be used as indicators of habitat change or degradation. Declines in neotropical migrants have been linked to changes in habitat quantity and quality across species' range. Songbirds that nest and forage in different habitat types or at different heights in the forest canopy may not be affected equally by forest change or management. We detected breeding songbirds using point-counts at Huntington Wildlife Forest (HWF) in the central Adirondack Mountains of New York during 1983-2000 and modeled on an original songbird point count dataset from Webb et al. (1977). Relative abundance (RA, the number of individual birds/count) was measured in sites with differing management histories, from an unmanaged >300-year-old stand to a stand cut with the shelterwood/overstory removal method just prior to sampling in 1983). Over eighty bird species were detected during the study duration. Songbird ecology and habitat characteristics can be used to understand long-term changes in relative abundance as related to forest change.
Breeding bird data using 50 m radius counting circles for the Parker River National Wildlife Refuge, Plum Island estuary, Massachusetts
This file contains breeding bird censuses using 50 m radius counting circles at locations on Plum Island, Massachusetts in the Parker River National Wildlife Refuge, Massachusetts.
SGS-LTER Avian Road Counts (Breeding Bird Survey) in eastern Colorado, USA 1994-2002
This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado. The data table and associated metadata document, which is in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. The Breeding Bird Survey is a large-scale survey of North American birds. It is a roadside survey, primarily covering the continental United States and southern Canada, although survey routes have recently been initiated in Alaska and northern Mexico. The BBS was started in 1966, and the over 3,500 routes are surveyed in June by experienced birders. Routes 305, Nunn and 901, Rockport are located in the area of the SGS research site. The primary objective of the BBS has been the estimation of population change for songbirds. However, the data have many potential uses, and investigators have used the data to address a variety of research and management objectives. In the USGS-BBS Home Page, reults from the BBS are summarized, and pictures of birds and other species information. Data from 1966 - 2002 were managed by the SGS-LTER project. Additional information and referenced materials can be found: http://hdl.handle.net/10217/82150.
Habitat suitability maps for boreal-breeding passerine species
<p><strong>About the Maps</strong></p> <p>Maps depict model-predicted species distribution and provide information about relative habitat suitability based on current climate and landcover. The suitability ranking of any mapped grid cell is the sum of the probabilities of that grid cell and all other grid cells with equal or lower probability, multiplied by 100 to give a percentage. This value represents the % of grid cells with a lower suitability value within the boreal/hemiboreal study region. Higher value pixels represent higher habitat suitability for a given species. Models do not account for physiographic barriers that may prevent colonization of otherwise suitable habitat, e.g., the Canadian Cordillera (<a href="#_ENREF_4">Erskine 1977</a>). Therefore actual species distributions may be over-estimated in certain regions, particularly in Alaska. </p> <p><strong>Modeling Overview</strong></p> <p>The maximum entropy (Maxent) method (<a href="#_ENREF_9">Phillips et al. 2006</a>, <a href="#_ENREF_10">Phillips and Dudik 2008</a>) was used to develop species distribution models (SDM) for passerine species during the breeding season. Maxent is a powerful machine-learning algorithm with demonstrated high predictive accuracy compared to other SDM methods (<a href="#_ENREF_3">Elith et al. 2006</a>). Although Maxent was developed for presence-only data (e.g., museum records), it is also appropriate for datasets compiled from disparate sources with varying levels of effort, such that information on species absence varies across model units. Although resulting predictions cannot be interpreted as probability of occurrence, they are robust representations of rank-order suitability. The power of Maxent lies in the complexity of relationships (e.g., non-linear, threshold, multiplicative) that it can readily handle, producing detailed, high-accuracy predictions.</p> <p>The key consideration in development of Maxent models, as with traditional resource selection functions (<a href="#_ENREF_8">Manly 1993</a>), is the selection of appropriate “background” data (<a href="#_ENREF_11">Phillips et al. 2009</a>). Otherwise, sample bias can lead to biased predictions. As recommended (<a href="#_ENREF_11">Phillips et al. 2009</a>), we constrained our background to all locations surveyed for birds. Due to high spatial aggregation of survey locations and the resulting potential for bias, we aggregated occurrence records at the level of 4-km grid cells corresponding with the resolution of our climate data. A species was considered present in a grid cell if at least one individual had been counted over all point-count surveys contained in the grid cell. Model background was thus defined as all surveyed 4-km grid cells (n = 29,059).</p> <p><strong>Climate Data</strong></p> <p>Climate variables were derived from 4-km monthly climate normals (1961-1990) based on a combination of PRISM (<a href="#_ENREF_2">Daly et al. 2002</a>) and WorldClim (<a href="#_ENREF_6">Hijmans et al. 2005</a>) climate data. The western North America portion of these data are described in Wang et al. (<a href="#_ENREF_12">2011</a>). We used a set of 17 derived bioclimatic variables presumed to adequately summarize climate conditions within the boreal forest region (Table 1 in report). We were not concerned with high correlation among these covariates because models were developed for prediction purposes only and our goal for this particular exercise was not to interpret the importance of individual covariates.</p> <p><strong>Landcover Data</strong></p> <p>Landcover data consisted of a 2005 classified landcover map of North America developed by the Council on Economic Development (<a href="http://www.cec.org/Page.asp?PageID=924&ContentID=2819">http://www.cec.org/Page.asp?PageID=924&ContentID=2819</a>). We used 15 of the 19 landcover classifications as inputs to bird models (Table 2 in report). Because landcover was mapped at a 250-m resolution, we summarized the proportion of each landcover type within a 4-km grid cell for prediction purposes. For model-building purposes, we summarized landcover proportions according to the distribution of survey locations within the 4-km grid cell. This was based on the landcover type at the point-count center, reflecting the dominant type surveyed.</p> <p><strong>Avian Data</strong></p> <p>Distribution models were developed for all passerine species (+ 2 non-passerine landbird species) with at least 100 occurrence records in separate 4-km grid cells (n=94). Avian occurrence records were obtained from two major datasets: (1) the Boreal Avian Modelling (BAM) point-count dataset (Cumming et al. 2010) and the North American Breeding Bird Survey (BBS) point-count dataset from USGS (<a href="http://www.pwrc.usgs.gov/bbs/">http://www.pwrc.usgs.gov/bbs/</a>). Due to large discrepancies in survey characteristics and species detectability, which have already been addressed for the purpose of density estimation (Sólymos et al. 2013), the focus here was on the occurrence portion of the dataset only. Future efforts will integrate detectability offsets into bioclimatic density models that can be used to generate regional abundance estimates.</p> <p>In order to improve model predictive power within the boreal forest region, data from neighboring hemiboreal regions were also incorporated (as well as data from arctic and mountain regions where possible). Because the core BAM dataset is largely restricted to the boreal forest region, ancillary data consisted primarily of point-level BBS data (breeding bird atlas datasets were notable exceptions). BBS data were obtained for the level 3 ecoregions (<a href="http://www.epa.gov/wed/pages/ecoregions/na_eco.htm#Level III">http://www.epa.gov/wed/pages/ecoregions/na_eco.htm#Level III</a>) that intersected the boundary of the combined Brandt (<a href="#_ENREF_1">2009</a>) boreal/hemiboreal boundary. This additional data improved coverage of climate and landcover conditions at species’ range limits, thereby providing more opportunities to detect differences in habitat suitability. A total of 117,179 point-count locations were used to summarize species occurrence within 29,059 surveyed grid cells. See Table 3 in report for numbers of individual species occurrence records.</p> <p><strong>Maxent Model Details and Accuracy Assessment</strong></p> <p>Models were developed using Maxent version 3.3.3e. We used the cumulative probability output format, allowed all feature types except hinge features, and used a regularization multiplier of 1. We ran the model 10 times using bootstrapped subsamples of the BAM/BBS dataset, each time holding out a random 50% for validation purposes (test data). Model predictions were averaged across the 10 bootstrap replicates. Although models were developed using data from outside of the Brandt boreal/hemiboreal boundary, predictions were constrained to this region..</p> <p>The accuracy of each model was assessed by calculating the area under the curve (AUC) of the receiver operating characteristic plot (<a href="#_ENREF_5">Fielding and Bell 1997</a>) based on test data. AUC values were also averaged across the 10 replicates. The AUC value can be interpreted as the likelihood that a randomly-selected presence location will have a higher suitability score than a randomly-selected background location. </p> <p>In general, models were reasonably accurate in their prediction of species’ distributions. Average AUC scores ranged from 0.56 for American Robin to 0.97 for American Tree Sparrow (Table 3). Across all 94 species, AUC scores averaged 0.81 ±0.09 (SD). Models for 31 species were considered acceptable 0.7 ≤ AUC < 0.8), 31 were excellent (0.8 ≤ AUC < 0.9), and 17 had outstanding discrimination ability (AUC ≥ 0.9) (<a href="#_ENREF_7">Hosmer and Lemeshow 1989</a>). AUC scores reflected the ability to discriminate among different levels of habitat suitability within the greater boreal/hemiboreal region. Thus, species with distinct range limits within this region were more accurately predicted.</p> <p><strong>NatureServe Comparisons</strong></p> <p>Models and occurrence records were overlaid with published range maps from NatureServe (<a href="http://datazone.birdlife.org/species/requestdis">http://datazone.birdlife.org/species/requestdis</a>) for comparison purposes. For all but three species, the BAM/BBS dataset contained occurrence records outside of NatureServe range map limits. This discrepancy is reflected in the Maxent model predictions. Thus, both occurrence records and model predictions may be used to refine the range limits for several species. All but nine species had data observations north of their published range limits. Although better range maps may exist for many species (e.g., in recently revised Birds of North America volumes, <a href="http://bna.birds.cornell.edu/bna/">http://bna.birds.cornell.edu/bna/</a>), digital versions are not generally available for comparison.</p> <p><strong>Literature Cited</strong></p> <p>Brandt, J. P. 2009. The extent of the North American boreal zone. Environmental Reviews <strong>17</strong>:101–161.</p> <p>Cumming, S. G., K. L. Lefevre, E. Bayne, T. Fontaine, F. K. A. Schmiegelow, and S. J. Song. 2010. Toward conservation of Canada's boreal forest avifauna: design and application of ecological models at continental extents. Avian Conservation and Ecology<strong> 5</strong>(2):8.</p> <p>Daly, C., W. P. Gibson, G. H. Taylor, G. L. Johnson, and P. Pasteris. 2002. A knowledge-based approach to the statistical mapping of climate. Climate Research <strong>22</strong>:99-113.</p> <p>Elith, J., C. H. Graham, R. P. Anderson, M. Dudik, S. Ferrier, A. Guisan, R. J. Hijmans, F. Huettmann, J. R. Leathwick, A. Lehmann, J. Li, L. G. Lohmann, B. A. Loiselle, G. Manion, C. Moritz, M. Nakamura, Y. Nakazawa, J. McC. M. Overton, A. Townsend Peterson, S. J. Phillips, K. Richardson, R. Scachetti-Pereira, R. E. Schapire, J. Soberón, S. Williams, M. S. Wisz, and N. E. Zimmermann. 2006. Novel methods improve prediction of species' distributions from occurrence data. Ecography <strong>29</strong>:129-151.</p> <p>Erskine, A. J. 1977. Birds in boreal Canada: communities, densities, and adaptations. Ottawa, Canada.</p> <p>Fielding, A. H. and J. F. Bell. 1997. A review of methods for the assessment of prediction errors in conservation presence/absence models. Environmental Conservation <strong>24</strong>:38-49.</p> <p>Hijmans, R. J., S. E. Cameron, J. L. Parra, P. G. Jones, and A. Jarvis. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology <strong>25</strong>:1965-1978.</p> <p>Hosmer, D. W. and S. Lemeshow. 1989. Applied logistic regression. John Wiley and Sons, New York.</p> <p>Manly, B. F. J. 1993. Resource Selection by Animals: Statistical Design and Analysis for Field Studies. Chapman and Hall, London.</p> <p>Phillips, S. J., R. P. Anderson, and R. E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling <strong>190</strong>:231-259.</p> <p>Phillips, S. J. and M. Dudik. 2008. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography <strong>31</strong>:161-175.</p> <p>Phillips, S. J., M. Dudik, J. Elith, C. H. Graham, A. Lehmann, J. Leathwick, and S. Ferrier. 2009. Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data. Ecological Applications <strong>19</strong>:181-197.</p> <p>Sólymos, P., S. M. Matsuoka, E. M. Bayne, S. R. Lele, P. Fontaine, S. G. Cumming, D. Stralberg, F. K. A. Schmiegelow, and S. J. Song. 2013. Calibrating indices of avian density from non-standardized survey data: making the most of a messy situation. Methods in Ecology and Evolution <strong>4</strong>:1047-1058.</p> <p>Wang, T., A. Hamann, D. L. Spittlehouse, and T. Q. Murdock. 2011. ClimateWNA-High-Resolution Spatial Climate Data for Western North America. Journal of Applied Meteorology and Climatology <strong>51</strong>.</p> <p> </p> <p> </p>
Data from: Colony size affects breeding density, but not spatial distribution type, in a seabird
<p>The spatial distribution of individuals within populations can result in fine-scale density-dependence and affect the social environment that is encountered. As such, it is important to quantify within-population spatial structuring and understand the factors that shape it. In this study, we make use of point process statistics to test whether colony size affects the statistical type of spatial nest distribution produced by common terns (<i>Sterna hirundo</i>) breeding at identical man-made rectangular and homogeneous islands of fixed physical size. Comparing sub-colonies of variable density both within and across years, we find that inter-nest distances are smaller at higher local and overall breeding density, but that the spatial distribution type does not vary across the observed densities. This suggests that the birds' main settlement rules do not depend on density. In our case, analyses of fine-scale density-dependence or potential social effects therefore do not need to account for between-individual heterogeneity in settlement decision rules or acceptance of these rules. We urge, however, other studies to similarly test for density-dependence of the spatial distribution of individuals before undertaking such 'down-stream' analyses.</p>
Data from: Understanding the social dynamics of breeding phenology: indirect genetic effects and assortative mating in a long distance migrant
Phenological traits, such as the timing of reproduction, are often influenced by social interactions between paired individuals. Such partner effects may occur when pair members affect each other's pre-breeding environment. Partner effects can be environmentally and/or genetically determined, and quantifying direct and indirect genetic effects is important for understanding the evolutionary dynamics of phenological traits. Here, using 26 years of data from a pedigreed population of a migratory seabird, the common tern ( Sterna hirundo ), we investigate male and female effects on female laying date. We find that female laying date harbors both genetic and environmental variation, and is additionally influenced by the environmental, and, to a lower extent, genetic, component of her mate. We demonstrate this partner effect to be largely explained by male arrival date. Interestingly, analyses of mating patterns with respect to arrival date show mating to be strongly assortative and, using simulations, we show that this assortative mating for arrival date leads to overestimation of partner effects. Our study provides evidence for partner effects on breeding phenology in a long distance migrant, while uncovering the potential causal pathways underlying the observed effects and raising awareness for confounding effects due to assortative mating or other common environmental effects.
Data from: Specialized breeding in plants affects diversification trajectories in Neotropical frogs
<p>Many animals breed exclusively in plants that accumulate rainwater (phytotelma; e.g., bromeliad, bamboo, fruit husk, and tree hole), to which they are either physiologically or behaviorally specialized for this microhabitat.<b> </b>Of the numerous life-history modes observed in frogs, few are as striking or potentially consequential as the transition from pond- or stream-breeding to the deposition of eggs or larvae in phytotelmata. Such specialization can increase offspring survivorship due to reduced competition and predation, representing potential ecological opportunity for adaptive radiation, yet few lineages of phytotelma-breeding frogs appear to have diversified extensively after such a transition, at least in the New World. We use a phylogeny of Neotropical frogs and data on breeding microhabitat to understand the evolutionary transitions involved with specialized phytotelma-breeding. First, we find that phytotelma-breeding is present in at least 168 species in 10 families of frogs. Across the phylogeny, we estimate 14 origins of phytotelma-breeding and 115 reversals, showing that phytotelma-breeding is a highly labile character. Second, phytotelma-breeding lineages overall have higher net diversification than non-phytotelma-breeding ones. This specialization represents an ecological opportunity resulting in increased diversification in most families with phytotelma-breeding lineages, whereas phytotelma-breeding toads have restricted diversification histories.</p>
Data from: Quantitative genetics of the use of conspecific and heterospecific social cues for breeding site choice
<p>Social information use for decision-making is common and affects ecological and evolutionary processes, including social aggregation, species coexistence and cultural evolution. Despite increasing ecological knowledge on social information use, very little is known about its genetic basis and therefore its evolutionary potential. Genetic variation in a trait affecting an individual's social and non-social environment may have important implications for population dynamics, interspecific interactions and for expression of other, environmentally plastic traits. We estimated repeatability, additive genetic variance and heritability of the use of conspecific and heterospecific social cues (abundance and breeding success) for breeding site choice in a population of wild collared flycatchers Ficedula albicollis. Repeatability was found for two social cues: previous year conspecific breeding success and previous year heterospecific abundance. Yet, additive genetic variances for these two social cues, and thus heritabilities, were low. This suggests that most of the phenotypic variation in the use of social cues and resulting conspecific and heterospecific social environment experienced by individuals in this population stems from phenotypic plasticity. Given the important role of social information use on ecological and evolutionary processes, more studies on genetic versus environmental determinism of social information use are needed.</p>
Data from: Using molecular and crowd-sourcing methods to assess breeding ground diet of a migratory brood parasite of conservation concern
<p>Breeding ground food availability is critical to the survival and productivity of adult birds. The common cuckoo <i>Cuculus canorus</i> is a brood-parasitic Afro-Palearctic migrant bird exhibiting long-term (breeding) population declines in many European countries. Variation in population trend between regions and habitats suggests breeding ground drivers such as adult food supply. However, cuckoo diet has not been studied in detail since before the most significant population declines in Europe began in the mid-1980s. 20th century studies of cuckoo diet largely comprised field observations likely to carry bias towards larger prey taxa. Here we demonstrate the potential value of 1) using high-throughput DNA sequencing of invertebrate prey in faeces to determine cuckoo diet with minimal bias towards large prey taxa, and 2) using crowd-sourced digital photographs from across Britain to identify lepidopteran cuckoo prey taxa during recent years post-decline (2005-2016). DNA analysis found a high frequency of Lepidoptera, including moths of family Lasiocampidae, prominent within the past literature, but also grasshoppers (Orthoptera) and flies (Diptera) that may be overlooked by field observation methodologies. The range of larval lepidopteran prey identified from photographs largely agreed with those previously documented, with potential signs of reduced diversity, and identities of key adult prey taxa were supported by molecular results. Notably, many identified cuckoo prey taxa have shown severe declines due to agricultural intensification, suggesting this has driven spatial patterns of cuckoo loss. Landscape-scale, lowland rewilding interventions provide opportunities to understand the scale of reversal of previous agricultural intensification that may be necessary to restore prey populations sufficiently to permit recolonization by cuckoos.</p>
Life history data for longer-lived tropical songbirds reduce breeding activity as they buffer impacts of drought
<p><span>Droughts are expected to increase in frequency and severity with climate change. Population impacts of such harsh environmental events are theorized to vary with life history strategies among species. However, existing demographic models generally do not consider behavioral plasticity that may modify the impact of harsh events. Here we show that tropical songbirds in the New and Old World reduced reproduction during drought, with greater reductions in species with higher average long-term survival. Large reductions in reproduction by longer-lived species were associated with higher survival during drought than pre-drought years in Malaysia, whereas shorter-lived species maintained reproduction and survival decreased. Behavioral strategies of longer-lived, but not shorter-lived, species mitigated the effect of increasing drought frequency on long-term population growth. Behavioral plasticity can buffer the impact of climate change on populations of some species, and differences in plasticity among species related to their life histories are critical for predicting population trajectories.</span></p>
Data from: Cascading effects of climate variability on the breeding success of an edge population of an apex predator
<p>1. Large-scale environmental forces can influence biodiversity at different levels of biological organization. Climate, in particular, is often associated to species distributions and diversity gradients. However, its mechanistic link to population dynamics is still poorly understood.</p> <p>2. Here, we unraveled the full mechanistic path by which a climatic driver, the Atlantic trade winds, determines the viability of a bird population.</p> <p>3. We monitored the breeding population of Eleonora's falcons in the Canary Islands for over a decade (2007-2017) and integrated different methods and data to reconstruct how the availability of their prey (migratory birds) is regulated by trade winds. We tracked foraging movements of breeding adults using GPS, monitored departure of migratory birds using weather radar, and simulated their migration trajectories using an individual-based, spatially explicit model.</p> <p>4. We demonstrate that regional easterly winds regulate the flux of migratory birds that is available to hunting falcons, determining food availability for their chicks and consequent breeding success. By reconstructing how migratory birds are pushed towards the Canary Islands by trade winds, we explain most of the variation (up to 86%) in annual productivity for over a decade.</p> <p>5. This study unequivocally illustrates how a climatic driver can influence local-scale demographic processes, while providing novel evidence of wind as a major determinant of population fitness in a top predator. 06-Jul-2020</p>
Data from: Shifts in timing and duration of breeding for 73 boreal bird species over four decades
<p>Breeding timed to match optimal resource abundance is vital for the successful reproduction of species, and breeding is therefore sensitive to environmental cues. As the timing of breeding shifts with a changing climate, this may not only affect the onset of breeding, but also its termination, and thus the length of the breeding period. We use an extensive dataset of over 820K nesting records of 73 bird species across the boreal region in Finland to probe for changes in the beginning, end, and duration of the breeding period over four decades (1975-2017). We uncover a general advance of breeding with a strong phylogenetic signal, but no systematic variation over space. Additionally, 31% of species contracted their breeding period in at least one bioclimatic zone, as the end of the breeding period advanced more than the beginning. We did not detect a statistical difference in phenological responses of species with combinations of different migratory strategy or number of broods. Nonetheless, we find systematic differences in species responses, as the contraction in the breeding period was found almost exclusively in resident and short-distance migrating species, which generally breed early in the season. Overall, changes in the timing and duration of reproduction may potentially lead to more broods co-occurring in the early breeding season – a critical time for species' reproductive success. Our findings highlight the importance of quantifying phenological change across species and over the entire season, to reveal shifts in the community-level distribution of bird reproduction.</p>
High temperatures drive offspring mortality in a cooperatively breeding bird
<p><span>An improved understanding of life history responses to current environmental variability is required to predict species-specific responses to anthopogenic climate change. Previous research has suggested that cooperation in social groups may buffer individuals against some of the negative effects of unpredictable climates. We use a 15-year dataset on a cooperative-breeding arid-zone bird, the southern pied babbler <i>Turdoides bicolor</i>, to test i) whether environmental conditions and group size correlate with survival of young during three development stages (egg, nestling, fledgling), and ii) whether group size mitigates the impacts of adverse environmental conditions on reproductive success. Exposure to high mean daily maximum temperatures (mean T<sub>max</sub>) during early development was associated with reduced survival probabilities of young in all three development stages. No young survived when mean T<sub>max </sub>> 38°C across all group sizes. Low reproductive success at high temperatures has broad implications for recruitment and population persistence in avian communities given the rapid pace of advancing climate change.<b> </b>That impacts of high temperatures were not moderated by group size, a somewhat unexpected result given prevailing theories around the influence of environmental uncertainty on the evolution of cooperation, suggests that cooperative breeding strategies are unlikely to be advantageous in the face of rapid anthropogenic climate change. </span><span>An improved understanding of life history responses to current environmental variability is required to predict species-specific responses to anthopogenic climate change. Previous research has suggested that cooperation in social groups may buffer individuals against some of the negative effects of unpredictable climates. We use a 15-year dataset on a cooperative-breeding arid-zone bird, the southern pied babbler <i>Turdoides bicolor</i>, to test i) whether environmental conditions and group size correlate with survival of young during three development stages (egg, nestling, fledgling), and ii) whether group size mitigates the impacts of adverse environmental conditions on reproductive success. Exposure to high mean daily maximum temperatures (mean T<sub>max</sub>) during early development was associated with reduced survival probabilities of young in all three development stages. No young survived when mean T<sub>max </sub>> 38°C across all group sizes. Low reproductive success at high temperatures has broad implications for recruitment and population persistence in avian communities given the rapid pace of advancing climate change.<b> </b>That impacts of high temperatures were not moderated by group size, a somewhat unexpected result given prevailing theories around the influence of environmental uncertainty on the evolution of cooperation, suggests that cooperative breeding strategies are unlikely to be advantageous in the face of rapid anthropogenic climate change. </span></p>
Dynamic shifts in social network structure and composition within a breeding hybrid population
1. Mating behavior and the timing of reproduction can inhibit genetic exchange between closely related species; however, these reproductive barriers are challenging to measure within natural populations. Social network analysis provides promising tools for studying the social context of hybridization, and the exchange of genetic variation, more generally. 2. We test how social networks within a hybrid population of California (Callipepla californica) and Gambel's quail (Callipepla gambelii) change over discrete periods of a breeding season. We assess patterns of phenotypic and genotypic assortment, and ask whether altered associations between individuals (association rewiring), or changes to the composition of the population (individual turnover) drive network dynamics. We use genetic data to test whether social associations and relatedness between individuals correlate with patterns of parentage within the hybrid population. 3. To achieve these aims, we combine RFID association data, phenotypic data, and genomic measures with social network analyses. We adopt methods from the ecological network literature to quantify shifts in network structure and to partition changes into those due to individual turnover and association rewiring. We integrate genomic data into networks as node-level attributes (ancestry) and edges (relatedness, parentage) to test links between social and parentage networks. 4. We show that rewiring of associations between individuals that persist across network periods, rather than individual turnover, drives the majority of the changes in network structure throughout the breeding season, and that the traits involved in phenotypic/genotypic assortment were highly dynamic over time. Social networks were randomly assorted based upon genetic ancestry, suggesting weak behavioral reproductive isolation within this hybrid population. Finally, we show that the strength of associations within the social network, but not levels of genetic relatedness, predict patterns of parentage. 5. Social networks play an important role in population processes such as the transmission of disease and information, yet there has been less focus on how networks influence the exchange of genetic variation. By integrating analyses of social structure, phenotypic assortment, and reproductive outcomes within a hybrid zone, we demonstrate the utility of social networks for analyzing links between social context and gene flow within wild populations. 08-Jul-2020
Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs
<p><i><span>Background</span></i></p> <p><span>The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in <i>de-novo</i> genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (<i>Penaeus monodon</i>) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq).</span></p> <p><i><span>Results</span></i></p> <p><span>Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7,542 high-quality SNPs were retained. From these, 4,236 high-quality genome-wide loci were selected for bates-probe development and 4,194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 </span>± 14.7 to 93.0% ± 3.5%<span>), </span>increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7<span>), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches.</span></p> <p><i><span>Conclusion</span></i></p> <p><span>Importantly, this assay equips the <em>P. monodon</em> industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as <em>P. monodon</em> breeding programs transition to undertaking genomic selection.</span></p>
Figure 1 in Breeding ecology of the fulvous parrotbill (Paradoxornis fulvifrons) in Wawushan Nature Reserve, Sichuan, China
Figure 1. Full clutch laid in the nest of fulvous parrotbills.
Data from: Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool-breeding amphibians
Metapopulation-structured species can be negatively affected when landscape fragmentation impairs connectivity. We investigated the effects of urbanization on genetic diversity and gene flow for two sympatric amphibian species, spotted salamanders (Ambystoma maculatum) and wood frogs (Lithobates sylvaticus), across a large (>35,000 km2) landscape in Maine, USA, containing numerous natural and anthropogenic gradients. Isolation by distance (IBD) patterns differed between the species. Spotted salamanders showed a linear and relatively high variance relationship between genetic and geographic distance (r = 0.057; p < 0.001); whereas, wood frogs exhibited a strongly non-linear and lower variance relationship (r = 0.429; p < 0.001). Scale dependence analysis of IBD found gene flow has its most predictable influence (strongest IBD correlations) at distances up to 9 km for spotted salamanders and up to 6 km for wood frogs. Estimated effective migration surfaces revealed contrasting patterns of high and low genetic diversity and gene flow between the two species. Population isolation, quantified as the mean IBD residuals for each population, was associated with local urbanization and less genetic diversity in both species. The influence of geographic proximity and urbanization on population connectivity was further supported by distance-based redundancy analysis and multiple matrix regression with randomization. Resistance surface modelling found interpopulation connectivity to be influenced by developed land cover, light roads, interstates, and topography for both species, plus secondary roads and rivers for wood frogs. Our results highlight the influence of anthropogenic landscape features within the context of natural features and broad spatial genetic patterns, in turn supporting the premise that while urbanization significantly restricts interpopulation connectivity for wood frogs and spotted salamanders, specific landscape elements have unique effects on these two sympatric species.
Code and data for: Familiarity breeds success: pairs that meet earlier experience increased breeding performance in a wild bird population
<p>This is a Data package that contains three separate datasets and the analysis code for a manuscript 'Familiarity breeds success: pairs that meet earlier experience increased breeding performance in a wild bird population '. The first Dataset (pairs_data_2007_10) and the second dataset (pairs_data_2011_14) contain the data used to analyse the influence of meeting time of a pair of Great tits (i.e. month in the first dataset, week in the second dataset, when a pair was first detected in a flock together) on different components of breeding success of a pair. The third dataset (meeting_and_divorce) was used to analyse whether meeting time of a pair (in winter prior to the breeding season t) influence the probability of a pair to stay together or separate (divorce) to the following breeding season (t+1).</p>
Data from: Low fitness at low latitudes: wintering in the tropics increases migratory delays and mortality rates in an arctic-breeding shorebird
<p>1. Evolutionary theories of seasonal migration generally assume that the costs of longer migrations are balanced by benefits at the non-breeding destinations. 2. We tested, and rejected, the null hypothesis of equal survival and timing of spring migration for High Arctic breeding sanderling Calidris alba using six and eight winter destinations between 55° N and 25° S, respectively. 3. Annual apparent survival was considerably lower for adult birds wintering in tropical West-Africa (Mauritania: 0.74 and Ghana: 0.75) than in three European sites (0.84, 0.84 and 0.87) and in subtropical Namibia (0.85). Moreover, compared with adults, second calendar-year sanderlings in the tropics, but not in Europe, often refrained from migrating north during the first possible breeding season. During northward migration, tropical-wintering sanderlings occurred at their final staging site in Iceland 5-15 days later than birds wintering further north or south. Namibia-wintering sanderlings tracked with solar geolocators only staged in West-Africa during southward migration. 4. The low annual survival, the later age of first northward migration and the later passage through Iceland during northward migration of tropical-wintering sanderlings, in addition to the skipping of this area during northward but not southward migration by Namibia-wintering sanderlings, all suggest they face issues during the late non-breeding season in West-Africa. 5. Migrating sanderlings defy long distances but may end up in winter areas with poor fitness prospects. We suggest that ecological conditions in tropical West-Africa make the fuelling prior to northward departure problematic. </p>
Estimating survival for elusive juvenile pond‐breeding salamanders
<p>Juvenile vital rates have important effects on population dynamics for many species, but this demographic is often difficult to locate and track. As such, we frequently lack reliable estimates of juvenile survival, which are necessary for accurately assessing population stability and potential management approaches to conserve biodiversity. We empirically estimated survival rates for elusive juveniles of 3 complex lifecycle species of salamanders (ringed salamander [<i>Ambystoma annulatum</i>]<i>, </i>spotted slamander<i> </i>[<i>A. maculatum</i>]<i>, </i>and small-mouthed slamander [<i>A. texanum</i>]) using 2 approaches. First, we conducted an 11-month mark-recapture study within semi-natural enclosures and used Bayesian Cormack-Jolly-Seber models to estimate survival and recapture probabilities. Second, we inferred the expected annual juvenile survival rate given published vital rates for pre-metamorphic and adult ambystomatids assuming stable population growth. For all 3 species, juvenile survival probabilities were constant across recapture occasions, while recapture probability estimates were time-dependent. Further, survival and recapture probabilities among study species did not significantly differ. Post-study sampling revealed that the initial study period median estimate of annual survival probability (0.39) underestimated the number of salamanders known alive at 11 months. We therefore appended approximately 1 year of opportunistic data, which produced a median annual survival probability of 0.50, encompassing salamanders that we knew to have been alive. Calculation from literature values suggested a mean annual terrestrial juvenile ambystomatid survival probability of 0.45. Similar results among our approaches indicated that juvenile survival estimates for the study species were robust and likely comparable to rates in nature. These estimates can now be confidently applied to research, monitoring, and management efforts for the study species and ecologically similar taxa. Our data indicated that similarly robust vital rate estimates for subsets of ecologically and phylogenetically similar species can provide reasonable surrogate demographic information to advance conservation efforts for data-deficient species.</p>
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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.