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opencc-zeroDec 2020View details →

Wader breeding densities across European habitats

<div> Wading birds can be found breeding in a myriad of habitats and ecosystems across Europe that vary widely in their land-use intensity. Over the past few decades, wader breeding populations have declined steeply in habitats ranging from natural undisturbed ecosystems to intensively managed farmland. Most conservation science has focused on factors determining local population size and trends which leave cross-continental patterns and the associated consequences for large-scale conservation strategies unexplored. Here, we review the key factors underlying population decline. We find land-use intensification in western Europe and mostly agricultural extensification and abandonment in northern, central and eastern Europe to be important drivers. Additionally, predation seems to have increased throughout the breeding range and across all habitats. Using collected breeding density data from published and grey literature, we explore habitat specificity of wader species and, of the most widely distributed species, how breeding densities change across a land-use intensity gradient. We found that two-thirds of all examined wader species have relatively narrow breeding habitat preferences, mostly in natural and undisturbed ecosystems, while the remaining species occurred in most or all habitats. The most widespread generalist species (black-tailed godwit, northern lapwing, common redshank, Eurasian oystercatcher, common snipe and ruff) demonstrated peak breeding densities at different positions along the land-use intensity gradient. To conserve both diverse wader communities and viable meta-populations of species, a diversity of habitats should be targeted ranging in land-use intensity from natural ecosystems to medium-intensity farmland. Alongside, strategies should be designed to moderate predation of wader clutches and chicks. </div>

opencc-zeroFeb 2022View details →

Data on range-wide breeding habitat use of the critically endangered Yellow-breasted Bunting Emberiza aureola after population collapse

The population of the Yellow-breasted Bunting Emberiza aureola, a formerly widely distributed and abundant songbird of northern Eurasia, suffered a catastrophic decline and a strong range contraction between 1980 and 2013. There is evidence that the decline was driven by illegal trapping during migration, but potential contributions of other factors to the decline, such as land-use change, have not yet been evaluated. Before effects of land-use change can be evaluated, a basic understanding of the ecological requirements of the species is needed. We therefore compared habitat use in ten remaining breeding regions across the range, from European Russia to Japan and the Russian Far East. We also assessed large-scale variation in habitat parameters across the breeding range. We found large variation in habitat use, within and between populations. Differences were related to the cover and height of trees and shrubs at Yellow-breasted Bunting territories. In many regions, Yellow-breasted Buntings occupied early successional stages, including anthropogenic habitats characterized by mowing, grazing or fire regimes. We found that the probability of presence can be best predicted with the cover of shrubs, herbs and grasses. Highest probabilities were found at shrub cover values of 40 to 70 %. Differences in habitat use along a longitudinal gradient were small, but we found strong differences across latitudes, possibly related to habitat availability. We conclude that the remaining Yellow-breasted Bunting populations are not limited to specific habitat types. Our results provide important baseline information to model the range-wide distribution of this critically endangered species and to guide targeted conservation measures.

Data for: Breeding honey bees (Apis mellifera L.) for low and high Varroa destructor population growth: gene expression of bees performing grooming behavior

Background Social organisms, including honey bees (Apis mellifera L.), have defense mechanisms to control the multiplication and transmission of parasites and pathogens within their colonies. Self-grooming, a mechanism of behavioral immunity, seems to contribute to restraining the population growth of the ectoparasitic mite Varroa destructor in honey bee colonies. Because V. destructor is the most damaging parasite of honey bees, breeding them for resistance against the mite is a high priority of the beekeeping industry. We conducted a bidirectional breeding program to select honey bee colonies with low and high varroa population growth (LVG and HVG, respectively). Having high and low lines of bees allowed the study of genetic mechanisms underlying self-grooming behavior between the extreme genotypes. Worker bees were classified into two categories: 'light groomers' and 'intense groomers'. The brains of bees from the different categories (LVG-intense, LVG-light, HVG-intense, and HVG-light) were used for gene expression and viral quantification analyses. Results Differentially expressed genes (DEGs) associated with the LVG and HVG lines were identified, including four odorant-binding proteins and a gustatory receptor. A functional enrichment analysis showed 19 enriched pathways from a list of 219 down-regulated DEGs in HVG bees, including the Kyoto Encyclopedia of Genes and Genomes (KEGG) term of oxidative phosphorylation. Additionally, bees from the HVG line showed higher levels of Apis rhabdovirus 1 and 2, Varroa destructor virus -1 (VDV-1), and Deformed wing virus-A (DWV-A) compared to bees of the LVG line. Conclusions The difference in expression of odorant-binding protein genes and a gustatory receptor between bee lines suggests a possible link between them and the perception of irritants to trigger rapid self-grooming instances that require the activation of energy metabolic pathways. Therefore, our results provide new insights into the molecular mechanisms involved in honey bee grooming behavior. Differences in viral levels in the brains of LVG and HVG bees showed the importance of investigating the pathogenicity and potential impacts of neurotropic viruses on behavioral immunity. The results of this study advance the understanding of a trait used for selective breeding, self-grooming, and the potential of using genomic-assisted selection to improve breeding programs.

Use of geolocators for investigating breeding ecology of a rock crevice-nesting seabird: method validation and impact assessment

1: Investigating ecology of marine animals, imposes a continuous challenge due to their temporal and/or spatial unavailability. Light-based geolocators (GLS) are animal-borne devices that provide relatively cheap and efficient method to track seabird movement and are commonly used to study migration. Here we explore the potential of GLS data to establish individual behaviour during the breeding period in a rock crevice-nesting seabird, the Little Auk, Alle alle. 2: By deploying GLS on 12 breeding pairs, we developed a methodological workflow to extract birds' behaviour from GLS data (nest attendance, colony attendance and foraging activity), and validated its accuracy using behaviour extracted from a well-established method based on video recordings. We also compared breeding outcome, as well as behavioural patterns of logged individuals with a control group treated similarly in all aspects except for the deployment of a logger, to assess short-term logger effects on fitness and behaviour. 3: We found a high accuracy of GLS-established behavioural patterns, especially during the incubation and early chick rearing period (when birds spend relatively long time in the nest). We observed no apparent effect of logger deployment on breeding outcome of logged pairs, but recorded some behavioural changes in logged individuals (longer incubation bouts and shorter foraging trips). 4: Our study provides a useful framework for establishing behavioural patterns (nest attendance and foraging) of a crevice-nesting seabird from GLS data (light and conductivity), especially during incubation and early chick rearing period. Given that GLS deployment does not seem to affect the breeding outcome of logged individuals but does affect fine-scale behaviour, our framework is likely to be applicable to a variety of crevice/burrow nesting seabirds, even though precautions should be taken to reduce deployment effect. Finally, because each species may have its own behavioural and ecological specificity, we recommend performing a pilot study before implementing the method in a new study system.

Are breeding activities risky for northern bobwhites? An assessment of survival costs of reproduction

Behaviors associated with breeding can increase mortality risk. This increased risk can be thought of as a cost of reproduction. Increased movements prior to breeding are common as individuals search for food and breeding sites. These increased movements are thought to entail greater predation risks as individuals travel through unfamiliar areas but few studies have looked at how these prebreeding movements affect survival, especially at a fine temporal resolution. Costs of reproduction may also occur during reproduction. For birds, incubation and brood-rearing can increase predation risk because individuals spend most of their time at nest sites or with broods, which may make them more easily detected and captured by predators. Using time- and individual-specific predictors of survival, I examined the relationship between survival, movements, habitat use, and breeding status of northern bobwhites Colinus virginianus in Colorado, USA. I found that prebreeding ranges were larger for breeders (29 ha) than non-breeders (18.7 ha) but daily movement distance was not different (163 m). Range size did not affect survival; however, longer recent daily movement distances (within 10 days) resulted in higher survival. Breeding status also affected survival; laying individuals experienced the highest daily survival rates followed by incubating, non-breeding and brood-rearing individuals. Overall, there appears to be a survival cost of reproduction for individuals during brood-rearing, but I found no evidence that increased movements results in decreased survival.

Data from: Helpers don't help when it's hot in a cooperatively breeding bird, the Southern Pied Babbler

Cooperative breeding, where more than two individuals invest in rearing a single brood, occurs in many bird species globally and often contributes to improved breeding outcomes. However, high temperatures are associated with poor breeding outcomes in many species, including cooperative species. We used data collected over three austral summer breeding seasons to investigate the contribution that helpers make to daytime incubation in a cooperatively breeding species, the Southern Pied Babbler Turdoides bicolor, and the ways in which their contribution is influenced by temperature. Helpers spent a significantly higher percentage of their time foraging (41.8 ± 13.7%) and a significantly lower percentage of their time incubating (18.5 ± 18.8%) than members of the breeding pair (31.3 ± 11% foraging & 37.4 ± 15.7% incubating). In groups with only one helper, the helper's contribution to incubation was similar to that of breeders. However, helpers in larger groups contributed less to incubation, individually, with some individuals investing no time in incubation on a given observation day. Helpers significantly decrease their investment in incubation on hot days (>35.5°C), while breeders tend to maintain incubation effort as temperatures increase. Our results demonstrate that pied babblers share the workload of incubation unequally between breeders and helpers, and this inequity is more pronounced during hot weather. These results may help to explain why recent studies have found that larger group size does not buffer against the impacts of high temperatures in this and other cooperatively breeding species.

opencc-zeroApr 2023View details →

Data from: Climate change consequences for differential adult survival and the mating system of a temperate breeding shorebird

Managing for the effects of climate change on species whose populations are currently imperiled requires detailed knowledge of the relationship between their demographic rates and climate variables. We sought this information for the West Coast breeding population of snowy plover (Charadrius nivosus), which was federally listed as threatened in 1993 due to substantial declines in the numbers of plovers breeding along the coast and in the number of sites occupied for breeding. Snowy plovers employ a serially polygamous breeding system in which the male typically tends chicks to independence. This unusual breeding system is favored by male-biased sex ratios in local populations. As part of a multi-species study of the effect of climate change on population growth, we used mark-capture models to examine climate drivers of adult survival for 1,219 snowy plovers banded at Monterey Bay over 38 years and known to overwinter on the surrounding north-central California outer coast. Non-climate variables, including sex and unmeasured annual mortality risks (e.g., predator abundance) were the primary factors affecting adult survival. However, there is evidence that cold weather, particularly extended cold snaps with daily low temperatures below 2˚C and daily high temperatures below 10˚C, decreases overwinter survival. Exceptionally cold winters had a particularly strong effect on adult female plovers, contributing to the male-biased adult sex ratios. Future winter climate on the north-central California coast is projected to be generally warmer with fewer and shorter cold snaps. Reduced mortality from cold winter weather may mitigate other threats faced by plovers, such as anthropogenically enhanced predator populations, habitat loss, and accelerated sea level rise, while altering the adult sex ratio and potentially shifting the evolutionary landscape maintaining the plover's unusual breeding system.

opencc-zeroApr 2023View details →

Data for: Mobilomes of four flower-breeding Drosophila species

Understanding the mechanisms that shape the architecture, diversity and adaptations of genomes and their ecological and genetic interfaces is of utmost importance to understand biological evolution. Transposable elements (TEs) play an important role in genome evolution, due to their ability to transpose within and between genomes, providing sites of non-allelic recombination. Here we investigate patterns and processes of TE driven genome evolution associated with niche diversification. Specifically, we compared TE content, TE landscapes, and frequency of horizontal transposon transfers (HTTs) across genomes of five flower-breeding Drosophila (FBD) with different levels of specialization on flowers. Further, we investigated whether niche breadth, and ecological and geographical overlaps are associated with potential for HTT rates. Mobilome landscapes recovered for all species presented a bell-shaped curve, revealing an equilibrium between transposition and excision over evolutionary history. This pattern agrees with results previously recovered for other Drosophilidae species of the same subgenera studied here, suggesting that lineage-specific factors shape the mobilome of this lineage. Nevertheless, the abundance and richness of TE superfamilies was associated with niche breadth. Furthermore, the two more widespread species, the specialist D. incompta and the generalist D. lutzii, presented the highest frequency of HTT events. Our analyses also revealed that HTT opportunities are positively influenced by abiotic niche overlap but are not associated with phylogenetic relationships, niche breadth and biotic niche overlap. This suggests the existence of intermediate vectors promoting HTTs between species presenting non-overlapping biotic niches.

opencc-zeroApr 2023View details →

Data for: The relationships of breeding stage to daytime singing behaviour and song perch height in Bermuda White-eyed Vireos (Vireo griseus bermudianus)

Bird song is crucial for attracting mates and defending territories, but different types of song or different singing behaviours may be involved in acquiring or maintaining each resource. Furthermore, male songbirds may adjust when and where they sing throughout the breeding season, depending on their breeding stage. However, such relationships remain untested in several avian taxa. Here, we studied male Bermuda White-eyed Vireos (Vireo griseus bermudianus), a passerine with two distinct song types (discrete and rambling), to test the mate attraction and territory defence hypotheses. We compare song production and song perch height among different stages of the breeding season and during the non-breeding season. We show that male vireos produce both song types during the breeding and non-breeding seasons, suggesting dual roles in mate choice and territorial defence. Song production did not differ significantly between the breeding and non-breeding seasons, but, within the breeding season, males without nesting duties sang significantly more songs than males with nesting duties. Song perch height was higher during the breeding season versus non-breeding season, among males without nesting duties compared to males with nesting duties, and when males produced discrete versus rambling songs. Our findings suggest that male vireos increase their conspicuousness to prospecting females by increasing song production and song perch height, and that they sing during the breeding and non-breeding seasons to defend year-round territories. Collectively, our study supports the mate attraction and territory defence hypotheses of bird song.

opencc-zeroMay 2023View details →

Chemical fingerprints indicate group membership in a highly social communal breeding bird

Gregarious species must distinguish group members from non-group members. Olfaction is important for group recognition in mammals but rarely studied in birds, despite birds using olfaction in social contexts from species discrimination to kin recognition. Olfactory-based recognition requires that groups have a signature odour, so we tested for preen oil and feather chemical similarity among group-living smooth-billed anis (Crotophaga ani). Physiology affects body chemistry, so we also tested for an effect of egg-laying competition, as a proxy for reproductive status, on female chemical similarity. Finally, the fermentation hypothesis for chemical recognition posits that host-associated microbes drive host odour, so we tested for covariation between ani chemicals and microbiota. Group members were more chemically similar than non-group members, regardless of body region, demonstrating that gregarious bird species can have group chemical signatures. Females in groups with less egg-laying competition had more similar preen oil, but not feather, chemicals, suggesting preen oil conveys information about reproductive status. There was no overall covariation between chemicals and microbes; instead, subsets of microbes could mediate olfactory cues in birds. Preen oil and feather chemicals showed little overlap, suggesting they convey different information. These findings will guide experimental work on olfaction in gregarious birds.

opencc-by-4.0Oct 2022View details →

Physiological impacts of chronic and experimental Plasmodium infection on breeding-condition male songbirds

This file contains data for an experimental inoculation project aimed at understanding physiological impacts of Plasmodium in breeding-condition songbirds. The 'readme' tab contains explanations for columns on each spreadsheet. We first compared metrics of health (mass, scaled mass, hematocrit, activity rate) and reproductive readiness (cloacal protuberance volume, maximum testosterone concentration in plasma) in male songbirds (Dark-eyed junco, Junco hyemalis hyemalis) with and without chronic Plamodium infections. Then, we quantified the change in these metrics following experimental inoculation with Plasmodium, and asked whether these changes varied between males with and without chronic Plasmodium infections.

opencc-zeroJun 2023View details →

Spring arrival of the common cuckoo at breeding grounds is strongly determined by environmental conditions in tropical Africa

Failure to adapt migration timing to changes in environmental conditions along migration routes and at breeding locations can result in mismatches across trophic levels, as occurs between the brood parasitic common cuckoo Cuculus canorus and its hosts. Using satellite tracking data from 87 male cuckoos across 11 years, we evaluate why the cuckoo has not advanced its arrival to the UK. Across years, breeding ground arrival was primarily determined by timing of departure from stopover in West Africa before northward crossing of the Sahara. Together with high population synchrony and low apparent endogenous control of this event, this suggests that a seasonal ecological constraint operating here limits overall variation in breeding grounds arrival, although this event was itself influenced by carry-over from timing of arrival into tropical Africa. Between-year variation within individuals was, in contrast, mostly determined by northward migration through Europe, likely due to weather conditions. We find evidence of increased mortality risk for a) early birds following migration periods positively impacting breeding grounds arrival, and b) late birds, possibly suffering energy limitation, after departure from the breeding grounds. These results help identify areas where demands of responding to global change can potentially be alleviated by improving stopover quality.

opencc-zeroJun 2023View details →

Breeding biology and nesting behaviour of the endemic subspecies of White-eyed Vireo (Vireo griseus bermudianus) on the Bermuda archipelago

See full abstract by searching the title of this article on the Journal of Field Ornithology webpage, ResearchGate, or Google Scholar.

opencc-by-4.0Jun 2023View details →

Impact of household bulky waste collection on the presence of dengue-transmitting mosquito breeding sites_dataset

The objective was to evaluate the impact of a municipal strategy to reduce Ae. aegypti in Asunción focused on the management of household bulky waste. To estimate the result, the Difference in Difference (DID) method was used. For the baseline, a simple random sampling of 324 households was carried out. The intervention implemented by the local government in an area with 180,000 residents, contributed to the collection of the equivalent of 14 kilos of bulky waste per inhabitant, given an idea of the magnitude of the problem. For the evaluation survey, 2.5 to 4 years after the intervention, 120 households were randomly selected, of which 60% had not been intervened (control households) and 40% had been intervened. As a result, a significant reduction was achieved in the total number of large solid waste found in the homes that were the object of the intervention. The differentiated collection was used mainly by those households that had a large number of large solid waste (DID of -55%), but not to get rid of all of these objects, but only a part. The data present no evidence of change in the percentage of households with breeding containers between the intervention and control groups.

opencc-by-4.0Jun 2023View details →

Supplementary data for "Genomic signatures of strawberry domestication and breeding" paper

<pre>############################################################################################ ## Supplementary data for "Genomic signatures of strawberry domestication and breeding" ## ## Author: Zhen Fan ## ## Date: 6/26/2023 ## ############################################################################################</pre> Octoploid strawberry SNP map (SNP.vcf.gz) includes filtered SNP using 289 individuals. GWAS_raw.zip includes raw data, BLUE estimates, genotyping data and marker positions for GWAS study of fruit size and yield.

opencc-zeroJun 2023View details →

Data for: Cavity-breeding birds create specific microhabitats for diverse arthropod communities in boreal forests

The nests of secondary cavity-nesters located in tree cavities may form specific microhabitats of conservation importance due to their limited accessibility and availability. Species-specific nesting materials in nests of different secondary cavity-nesters may furthermore provide very different microhabitats for arthropods. The potential differences in arthropod communities inhabiting nests of different bird species in excavated cavities or nest boxes have, however, rarely been studied despite their relevance for conservation. Here we investigated the diversity and composition of arthropod communities in these different cavity types and bird species' nests in managed boreal forests. We identified morphologically and by DNA-metabarcoding arthropods in nest materials that were collected in and compared between i) woodpecker-size cavities from seven different combinations of cavity type (nest box or excavated cavity), tree species (aspen or pine) and accumulation history of nest materials (single-season cleaned or uncleaned nest boxes that accumulated nests of passerines or an owl species); and ii) nests of two different passerine species in small nest boxes. We identified 64 arthropod taxa in ten orders, from which Diptera, Coleoptera, Siphonaptera, and Lepidoptera were the most abundant. Shannon diversity index was similar among the cavity-nest-type combinations, but taxa richness was the highest in the owl nests. The arthropod communities (especially Histeridae beetles) deviated most from the other types of nests in owl and aspen cavity nests with more advanced decomposition of nest material (soil or wet environment-related taxa). The differences in arthropod communities between the different nest types point out the importance of the ecological chain "tree cavities – bird nests – arthropod communities".

opencc-zeroJul 2023View details →

Genetic erosion in an endangered desert fish during a multi-decadal megadrought despite long-term supportive breeding

Human water use combined with a recent megadrought have reduced river and stream flow through the Southwestern United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande Silvery Minnow. This species experiences 'boom-and-bust' population dynamics where large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We leveraged demographic and genetic data from wild and hatchery individuals to understand the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d=1.34) and remains low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size (NeD) were positively associated (r=0.53) with wild/total abundance, but as the proportion of hatchery-origin spawners increased, NeD was reduced (NeD r= -0.55). Megadrought limits wild spawner abundance and precludes refreshment of hatchery brood stocks with wild fish, hence we predict an increasingly hatchery-dominated population, and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.

opencc-zeroAug 2023View details →

Instituto Nacional de Investigación Agropecuaria (INIA) Rice Breeding Program Historical Dataset

Breeding programs generate vast amounts of data which are often scattered in separate files. This hinders the application of modern breeding tools such as multi-environment analyses and genomic selection. This dataset is the result of consolidating 23 years of phenotypic, pedigree, and genomic records from the Uruguayan national rice breeding program. All the available data from 1997 to 2020 corresponding to field trials, blast nurseries, laboratory analyses of milling and cooking quality, pedigree information, and genomic information for selected advanced breeding lines are gathered. Records of 996 trials in 12 locations over a span of 23 years, 91,636 field plots with information on 14 phenotypic variables, pedigree for 19,447 genotypes, and genomic information regarding 61,260 SNP markers for 965 genotypes were recovered. The dataset is structured in Trials, Phenotypes, Lines, Genomic Information, and SNP Tables. Genotype identification has been coded.

opencc-zeroAug 2023View details →

Data for: Leveraging spatio-temporal genomic breeding value estimates of dry matter yield and herbage quality in ryegrass via random regression models

Joint modeling of correlated multi-environment and multi-harvest data of perennial crop species may offer advantages in prediction schemes and a better understanding of the underlying dynamics in space and time. The goal of the present study was to investigate the relevance of incorporating the longitudinal dimension of within-season multiple measurements of forage perennial ryegrass traits in a reaction norm model setup that additionally accounts for genotype-environment interactions (G×E). Genetic parameters and accuracy of genomic breeding value (gEBV) predictions were investigated by fitting three random regression models (gRRM) using Legendre polynomial functions to the data. Genomic DNA sequencing of family pools of diploid perennial ryegrass was performed using DNA nanoball-based technology and yielded 56,645 single nucleotide polymorphisms which were used to calculate the allele frequency-based genomic relationship matrix. Biomass yield's estimated additive genetic variance and heritability values were higher in later harvests. The additive genetic correlations were moderate to low in early measurements and peaked at intermediates, with fairly stable values across the environmental gradient, except for the initial harvest data collection. This led to the conclusion that complex (G×E) arises from spatial and temporal dimensions in the early season, with lower re-ranking trends thereafter. In general, modeling the temporal dimension with a second-order orthogonal polynomial improved the accuracy of gEBV prediction for nutritive quality traits, but no gain in prediction accuracy was detected for dry matter yield. This study leverages the flexibility and usefulness of gRRM models for perennial ryegrass breeding and can be readily extended to other multi-harvest crops.