Find research datasets worth reusing

opencc-by-nc-4.0Nov 2020View details →

Figure 1 in Breeding review of Gray-hooded Gull Chroicocephalus cirrocephalus in Brazil with contributions on nests and egg biometry

Figure 1. Breeding records of the Gray-hooded Gull (Chroicocephalus cirrocephalus) in Brazil. Nests (circles), breeding pairs (triangle), fledging chicks (square).

opencc-zeroDec 2013View details →

Data from: Mid-winter temperatures, not spring temperatures, predict breeding phenology in the European starling Sturnus vulgaris

In many species, empirical data suggest that temperatures less than 1 month before breeding strongly influence laying date, consistent with predictions that short lag times between cue and response are more reliable, decreasing the chance of mismatch with prey. Here we show in European starlings (Sturnus vulgaris) that mid-winter temperature ca 50–90 days before laying (8 January–22 February) strongly (r2 = 0.89) predicts annual variation in laying date. Mid-winter temperature also correlated highly with relative clutch size: birds laid later, but laid larger clutches, in years when mid-winter temperatures were lower. Despite a high degree of breeding synchrony (mean laying date 5–13 April = ±4 days; 80% of nests laid within 4.8 days within year), European starlings show strong date-dependent variation in clutch size and productivity, but this appears to be mediated by a different temporal mechanism for integration of supplemental cue (temperature) information. We suggest the relationship between mid-winter temperature and breeding phenology might be indirect with both components correlating with a third factor: temperature-dependent development of the starling's insect (tipulid) prey. Mid-winter temperatures might set the trajectory of growth and final biomass of tipulid larvae, with this temperature cue providing starlings with information on breeding season prey availability (though exactly how remains unknown).

Data from: Landscape genetic inferences vary with sampling scenario for a pond breeding amphibian

A critical decision in landscape genetic studies is whether to use individuals or populations as the sampling unit. This decision affects the time and cost of sampling and may affect ecological inference. We analyzed 334 Columbia spotted frogs at 8 microsatellite loci across 40 sites in northern Idaho to determine how inferences from landscape genetic analyses would vary with sampling design. At all sites, we compared a proportion available sampling scheme (PASS), in which all samples were used, to resampled datasets of 2-11 individuals. Additionally, we compared a population sampling scheme (PSS) to an individual sampling scheme (ISS) at 18 sites with sufficient sample size. We applied an information theoretic approach with both restricted maximum likelihood and maximum likelihood estimation to evaluate competing landscape resistance hypotheses. We found that PSS supported a low-density forest model (0.87) and ISS supported this model as well as additional models when testing hypotheses of landcover types that create the greatest resistance to gene flow for Columbia spotted frogs. Increased sampling density and study extent, seen by comparing PSS to PASS, showed a change in model support from a model of only low-density forest to a model of only high-density forest. As number of individuals increased, model support converged at 7 individuals for ISS to PSS. ISS may be useful to increase study extent and sampling density, but may lack power to provide strong support for the correct model with microsatellite datasets. Our results highlight the importance of additional research on sampling design effects on landscape genetics inference.

Data from: Age-related variation in non-breeding foraging behaviour and carry-over effects on fitness in an extremely long-lived bird

1. Senescence has been widely documented in wild vertebrate populations, yet the proximate drivers of age-related declines in breeding success, including allocation trade-offs and links with foraging performance, are poorly understood. For long-lived, migratory species, the non-breeding period represents a critical time for investment in self-maintenance and restoration of body condition, which in many species is linked to fitness. However, the relationships between age, non-breeding foraging behaviour and fitness remain largely unexplored. 2. We performed a cross-sectional study, investigating age-related variation in the foraging activity, distribution and diet of an extremely long-lived seabird, the wandering albatross Diomedea exulans during the non-breeding period, and its links with subsequent reproductive performance. 3. We tracked the distributions of 82 adults aged 8 – 33 years with geolocator-immersion loggers and found an age-related decline in the number of landings (a proxy of foraging effort) during daylight hours. There was a decrease in body feather δ13C values in older males but not females, yet this did not accompany an age-related shift in distributions. Males conducted fewer landings than females, and the sexes were spatially segregated, with males foraging further south, likely due to their differential utilization of winds. 4. While younger (< 20 years) birds had higher foraging activity, all individuals went on to breed successfully the following season. In contrast, among older (20+ years) birds, individuals that landed more often were more likely to defer breeding or fail during incubation, suggesting they have lower foraging success. 5. As far as we are aware, this is the first demonstration of an age-specific carry-over effect of foraging behaviour in the non-breeding period on subsequent reproductive performance. This link between foraging behaviour and fitness in late but not early adulthood indicates that the ability of individuals to forage efficiently outside the breeding period may be an important driver of fitness differences in old age.

Data from: Causes of seasonal decline in reproduction of the cooperatively-breeding acorn woodpecker

Clutch size and reproductive success decline seasonally in a wide range of temperate avian taxa. Two competing hypotheses have been proposed to explain such declines: the "timing" hypothesis, which states that conditions affecting reproduction decline intrinsically with date, and the "quality" hypothesis, which proposes that high-quality individuals or individuals in high-quality situations breed earlier. We contrasted the relative importance of these two hypotheses using a long-term dataset of the cooperatively-breeding acorn woodpecker (Melanerpes formicivorus) in central coastal California (USA). This population exhibits an 11% seasonal decline in clutch size, a 60% seasonal decline in fledging success, and a 77% seasonal decline in fledgling overwinter survival. Clutch size tracks seasonal availability of flying insects, which are a likely ecological driver of the seasonal decline in reproduction and, because of the nonlinear relationship of flying insects with date, constitute a likely factor constraining even earlier nesting. By parsing lay date data into within-female and between-female components, we found that only the within-female component had a statistically significant direct effect on clutch size, supporting the timing hypothesis. For both fledging success and overwinter survival, however, both within- and between-female effects were highly significant, with between-female effects (differences in female quality) being stronger than within-female effects. These results suggest that timing per se is a key factor affecting the seasonal decline in clutch size, but that both differences in female quality and an intrinsic seasonal decline in conditions drive the even more dramatic seasonal declines in fledging success and overwinter survivorship of fledglings.

Data from: Breeding season length and nest mortality drive cryptic life history variation in Dark-eyed Juncos (Junco hyemalis) breeding across a montane elevation gradient

The manner in which individual life history traits respond to the environment and to each other, and how these traits combine to form overall patterns of life history variation, remains poorly characterized in wild populations. We monitored breeding Dark-eyed Juncos (Junco hyemalis) across a 700-m elevational range. We compared breeding season length, temporal patterns of breeding activity, adult body size, clutch size, brood size, nestling quality, and nest mortality among elevations. We also compared environmental measures across the studied elevations to determine whether abiotic factors explained life history trait variation. We used 12 microsatellite loci to test for genetic differentiation in populations at different elevations. Finally, we constructed a computer simulation to evaluate the combined effects of observed variation in life history traits. We found differences among elevations in breeding season length and in patterns of reproductive timing, which did not match each other and which were not explained solely by abiotic factors. We found no differences among elevations in adult body size, clutch size, brood size, or nestling quality. Nest mortality increased significantly with elevation. Genetic differentiation was too low to define distinct subpopulations. The simulation suggested that differences in mortality, in combination with differences in breeding season length, contributed to substantial differences in reproductive success among elevations. Thus, although individual life history traits showed little evidence of variation in response to the environment or to each other and little genetic differentiation, variation in breeding season length and in nest mortality were potential drivers of substantial elevational variation in overall life history in this system. These results demonstrate that individual life history traits may vary substantially in their patterns of variation, and that some life history traits may have disproportionate effects on overall life history.

opencc-zeroJun 2019View details →

Data from: Large-scale manipulation of the acoustic environment can alter the abundance of breeding birds: evidence from a phantom natural gas field

1. Altered animal distributions are a consequence of human expansion and development. Anthropogenic noise can be an important predictor of abundance declines near human infrastructure, yet more information is needed to understand noise impacts at the spatial and temporal scales necessary to alter populations. 2. Energy development and associated anthropogenic noise are globally pervasive, and expanding. For example, 600,000 new natural gas wells have been drilled across central North America in less than twenty years. 3. We experimentally broadcast energy sector noise (recordings of compressor engines) in Southwest Idaho (USA). We placed arrays of speakers creating a "phantom natural gas field" in a large-scale experiment, and tested the effects of noise alone on breeding songbird abundance. To examine variation in human-caused noise, we broadcast two types of compressor noise, one with a slightly higher sound intensity and greater bandwidth than the other. 4. Our phantom natural gas field encompassed approximately 100 km2. We broadcast noise for over three continuous months, for each of two seasons, and quantified over 20,000 hours of background sound levels. 5. Brewer's sparrows (Spizella breweri) were affected by our narrowband playback, declining 30% 50 m from the speaker arrays. During our broadband playback, all species combined and Brewer's sparrows decreased 20% and 33% respectively at the scale of our sites (~0.5 km2; up to 400 m from speaker arrays). 6. Our results show the importance of incorporating the acoustic structure of noise when estimating the cost of noise exposure for populations and suggest an urgent need for noise mitigation, such as quieting compressor station noise, in energy extraction fields and natural areas broadly.

opencc-zeroDec 2016View details →

Data from: Phylogenetic relationships, breeding implications, and cultivation history of Hawaiian taro (Colocasia esculenta) through genome-wide SNP genotyping

Taro, Colocasia esculenta, is one of the world's oldest root crops and of particular economic and cultural significance in Hawai'i, where historically more than 150 different landraces were grown. We developed a genome-wide set of more than 2400 high-quality single nucleotide polymorphism (SNP) markers from 70 taro accessions of Hawaiian, South Pacific, Palauan, and mainland Asian origins, with several objectives: (a) uncover the phylogenetic relationships between Hawaiian and other Pacific landraces, (b) shed light on the history of taro cultivation in Hawai'i, and (c) develop a tool to discriminate among Hawaiian and other taros. We found that almost all existing Hawaiian landraces fall into five monophyletic groups that are largely consistent with the traditional Hawaiian classification based on morphological characters, e.g., leaf shape and petiole color. Genetic diversity was low within these clades but considerably higher between them. Population structure analyses further indicated that the diversification of taro in Hawai'i most likely occurred by a combination of frequent somatic mutation and occasional hybridization. Unexpectedly, the South Pacific accessions were found nested within the clades mainly composed of Hawaiian accessions, rather than paraphyletic to them. This suggests that the origin of clades identified here preceded the colonization of Hawai'i, and that early Polynesian settlers brought taro landraces from different clades with them. In the absence of a sequenced genome, this marker set provides a valuable resource towards obtaining a genetic linkage map, and to study the genetic basis of phenotypic traits of interest to taro breeding such as disease resistance.

opencc-zeroApr 2020View details →

Data from: Geographic variation in adult and embryonic desiccation tolerance in a terrestrial-breeding frog

Intra-specific variation in the ability of individuals to tolerate environmental perturbations is often neglected when considering the impacts of climate change. Yet this information is potentially crucial for mitigating deleterious effects of climate change on threatened species. Here we assessed patterns of intra-specific variation in desiccation tolerance in the frog Pseudophryne guentheri, a terrestrial-breeding species experiencing a drying climate. Adult frogs were collected from six populations across a rainfall gradient and their dehydration and rehydration rates were assessed. We also compared desiccation tolerance of embryos and hatchlings originating from within-population parental crosses from four of the populations. Embryos were reared on soil at three soil-water potentials and their desiccation tolerance was assessed across a range of traits. We found significant and strong patterns of intra-specific variation in almost all traits, both in adults and first-generation offspring. Adult frogs exhibited clinal variation in their water balance responses, with populations from drier sites both dehydrating and rehydrating more slowly compared to frogs from more mesic sites. Similarly, desiccation tolerance of first-generation offspring was significantly greater in populations from xeric sites. Our findings suggest that populations within this species will respond differently to the regional reduction in rainfall predicted by climate change models.

opencc-zeroApr 2020View details →

Data from: It's not all about temperature: breeding success also affects nest design

There are numerous observational studies on intra-specific variation in avian nest building and a single experimental manipulation. The general consensus is that birds build nests in response to environmental conditions, but it is not clear whether such flexibility in nest building is reproductively advantageous. To test the relationship between building flexibility and reproductive success, we allowed captive zebra finches to build their first nest, using string, and to breed in temperature-controlled rooms held at 14oC or 30oC. Once the offspring had fledged, we returned half the pairs to breed at the same temperature while half the pairs were switched to the alternative temperature. We provided all pairs with string and left them to build and breed a second time. For their first nest, pairs that built at 14°C used more string than did pairs that built at 30°C, and pairs that bred successfully built a nest with more string than did unsuccessful pairs. When pairs built their second nest, however, temperature no longer explained the number of pieces of string they used; rather, irrespective of the ambient temperature, pairs that had successfully produced young from their first nest used the same amount of string for their second nest while those that had failed to reproduce with their first nest used more string. These latter pairs were then more likely to reproduce successfully. Ambient temperature, therefore, did affect the nest the pairs built, but only in the absence of reproductive experience.

opencc-zeroMar 2020View details →

Investigating social and environmental predictors of natal dispersal in a cooperative breeding bird

Natal dispersal is a crucial life history trait that affects both individual fitness and population structure, yet drivers of variation in dispersal probability and distance are difficult to study in wild populations. In cooperatively breeding species, individuals typically delay dispersal beyond their first breeding season and remain on the natal territory as nonbreeders, which prolongs social dynamics that can affect dispersal decisions. Using a 35-year data set covering almost 600 dispersal events in the cooperatively breeding Florida scrub-jay (Aphelocoma coerulescens), we examined the environmental and social parameters that predict dispersal probability over time and distance. In both sexes, dispersal probability increased with age, which in turn was negatively correlated with dispersal distance. In males, individuals occupying low quality natal territories and living with a stepfather had an increased probability of dispersal. Older and more dominant males were more likely to inherit their natal territory. In females, which generally disperse earlier and farther than males, socially subordinate jays dispersed farther than dominant ones. Overall, jays that delayed dispersal the longest were more likely to attain breeding status near their natal territory, which was previously found to be associated with increased survival and lifetime fitness. Our results suggest that social dynamics and environmental factors on the natal territory affect delayed dispersal patterns differently for the two sexes in this cooperative breeder.

opencc-zeroApr 2020View details →

Data from: Deciphering genetic mate choice: not so simple in group-housed conservation breeding programs

Incorporating mate choice into conservation breeding programs can improve reproduction and the retention of natural behaviours. However, different types of genetic-based mate choice can have varied consequences for genetic diversity management. As a result, it is important to examine mechanisms of mate choice in captivity to assess its costs and benefits. Most research in this area has focused on experimental pairing trials, however this resource-intensive approach is not always feasible in captive settings and can interfere with other management constraints. We used generalised linear mixed models and permutation approaches to investigate overall breeding success in group-housed Tasmanian devils at three non-mutually exclusive mate choice hypotheses: (i) advantage of heterozygous individuals, (ii) advantage of dissimilar mates, and (iii) optimum genetic distance, using both 1,948 genome-wide SNPs and 12 MHC-linked microsatellites. The managed devil insurance population is the largest such breeding program in Australia and is known to have high variance in reproductive success. We found that non-genetic factors such as age were the best predictors of breeding success in a competitive breeding scenario, with younger females and older males being more successful. We found no evidence of mate choice under the hypotheses tested. Mate choice varies among species and across environments, so we advocate for more studies in realistic captive management contexts as experimental or wild studies may not apply. Conservation managers must weigh up the need to wait for adequate sample sizes to detect mate choice with the risk that genetic changes may occur during this time in captivity. Our study shows that examining and integrating mate choice into the captive management of species housed in realistic, semi-natural group-based contexts may be more difficult than previously considered.

Data from: Consequences of breeding system for body condition and survival throughout the annual cycle of tidal marsh sparrows

An individual's body condition and probability of survival can change throughout the annual cycle, based on the combined effects of many factors, including reproductive investment during breeding, colder temperatures during winter, and elevated risks during migration. We evaluated body condition and survival during breeding and non-breeding periods in two closely related species with notably different reproductive systems. Male and female saltmarsh sparrows (Ammodramus caudacutus) represent extremes in parental care: males perform none, leaving females to do everything from build nests to care for fledglings. In contrast, male and female seaside sparrows (A. maritimus) have bi-parental care and similar levels of reproductive investment, intermediate between male and female saltmarsh sparrows. Our results are consistent with the idea that females experience non-lethal effects of reproduction, and that differences between the breeding season and winter affect condition. In both species, females had lower scaled mass index (SMI) values than males during both breeding and non-breeding seasons, and female saltmarsh sparrows had lower SMI values than female seaside sparrows. Females carried more fat than males during the breeding season, and female, but not male, fat and muscle scores decreased over time, which is consistent with the adaptive mass hypothesis. In winter, all groups carried more fat and had higher muscle scores than when breeding, despite having lower SMI scores. Although we observed variation in body condition, within-season survival was uniformly high in both seasons, suggesting that sex, species, season, body size, and body condition have little impacts on within season survival. Comparisons with previously-published estimates of annual adult survival suggest that most mortality occurs during migration, even in these short-distance migrants. The importance of considering multiple aspects of body condition, multiple seasons, and difficult-to-monitor events, such as migration, should not be ignored when thinking about the events and processes that cumulatively determine population dynamics.

Data from: Rethinking 'normal': the role of stochasticity in the phenology of a synchronously breeding seabird

1. Phenological changes have been observed in a variety of systems over the past century. There is concern that, as a consequence, ecological interactions are becoming increasingly mismatched in time, with negative consequences for ecological function. 2. Significant spatial heterogeneity (inter-site) and temporal variability (inter-annual) can make it difficult to separate intrinsic, extrinsic, and stochastic drivers of phenological variability. The goal of this study was to understand the timing and variability of breeding phenology of Adélie penguins under fixed environmental conditions, and to use those data to identify a 'null model' appropriate for disentangling the sources of variation in wild populations. 3. Data on clutch initiation were collected from both wild and captive populations of Adélie penguins. Clutch initiation in the captive population was modeled as a function of year, individual, and age to better understand phenological patterns observed in the wild population. 4. Captive populations displayed as much inter-annual variability in breeding phenology as wild populations, suggesting that variability in breeding phenology is the norm and thus may be an unreliable indicator of environmental forcing. The distribution of clutch initiation dates was found to be moderately asymmetric (right skewed) both in the wild and in captivity, consistent with the pattern expected under social facilitation. 5. The role of stochasticity in phenological processes has heretofore been largely ignored. However, these results suggest that inter-annual variability in breeding phenology can arise independent of any environmental or demographic drivers and that synchronous breeding can enhance inherent stochasticity. This complicates efforts to relate phenological variation to environmental variability in the wild. Accordingly, we must be careful to consider random forcing in phenological processes, lest we fit models to data dominated by random noise. This is particularly true for colonial species where breeding synchrony may outweigh each individual's effort to time breeding with optimal environmental conditions. Our study highlights the importance of identifying appropriate null models for studying phenology.

opencc-zeroDec 2019View details →

Sex-independent senescence in a cooperatively breeding mammal

1. Researchers studying mammals have frequently interpreted earlier or faster rates of ageing in males as resulting from polygyny and the associated higher costs of reproductive competition. 2. Yet few studies conducted on wild populations have compared sex-specific senescence trajectories outside of polygynous species, making it difficult to make generalised inferences on the role of reproductive competition in driving senescence, particularly when other differences between males and females might also contribute to sex-specific changes in performance across lifespan. 3. Here, we examine age-related variation in body mass, reproductive output and survival in dominant male and female meerkats, Suricata suricatta. Meerkats are socially monogamous cooperative breeders where a single dominant pair virtually monopolize reproduction in each group and subordinate group members help to rear offspring produced by breeders. 4. In contrast to many polygynous societies, we find that neither the onset nor the rate of senescence in body mass or reproductive output show clear differences between males and females. Both sexes also display similar patterns of age-related survival across lifespan, but unlike most wild vertebrates, survival senescence (increases in annual mortality with rising age) was absent in dominants of both sexes, and as a result, the fitness costs of senescence were entirely attributable to declines in reproductive output from mid- to late-life. 5. We suggest that the potential for intrasexual competition to increase rates of senescence in females – who are hormonally masculinised and frequently aggressive – is offset by their ability to maintain longer tenures of dominance than males, and that these processes combined lead to similar patterns of senescence in both sexes. 6. Our results stress the need to consider the form and intensity of sexual competition as well as other sex-specific features of life history when investigating the operation of senescence in wild populations.

opencc-by-4.0Dec 2016View details →

Simulated breed for GENMON

This file contains a pedigree from a simulated breed. It is intended to be run with GENMON

opencc-zeroNov 2023View details →

Mapping multiscale breeding bird species distributions across the United States and evaluating their conservation applications

Species distribution models are vital to management decisions that require understanding habitat use patterns, particularly for species of conservation concern. However, the production of distribution maps for individual species is often hampered by data scarcity, and existing species maps are rarely spatially validated due to limited occurrence data. Furthermore, community-level maps based on stacked species distribution models lack important community assemblage information (e.g., competitive exclusion) relevant to conservation. Thus, multispecies, guild, or community models are often used in conservation practice instead. To address these limitations, we aimed to generate fine-scale, spatially-continuous, nationwide maps for species represented in the North American Breeding Bird Survey (BBS) between 1992-2019. We generated ensemble models for each species at three spatial resolutions – 0.5, 2.5, and 5 km – across the conterminous United States. We also compared species richness patterns from stacked single-species models with those of 19 functional guilds developed using the same data to assess the similarity between predictions. We successfully modeled 192 bird species at 5-km resolution, 160 species at 2.5-km resolution, and 80 species at 0.5-km resolution. However, the species we could model represent only 28-56% of species found in the conterminous US BBS surveys across resolutions owing to data limitations. We found stacked maps and guild maps generally had high correlations across resolutions (median = 84%), but spatial agreement varied regionally by resolution and was most pronounced between the East and West at the 5-km resolution. The spatial differences between our stacked maps and guild maps illustrate the importance of spatial validation in conservation planning. Overall, our species maps are useful for single-species conservation and can support fine-scale decision-making across the United States, and can also support community-level conservation when used in tandem with guild maps. However, there are still data scarcity issues for many species of conservation concern when using the BBS for single-species models.

opencc-by-4.0Apr 2020View details →

Fig. 10 in Distribution, systematics and nomenclature of the three taxa of Common Stonechats (Aves, Passeriformes, Muscicapidae, Saxicola) that breed in the Caucasian region

Fig. 10. Drawing of Parus variegatus Gmelin, 1774, after Ivan Borisov's watercolour (Taf. 20, 3 R).

opencc-by-4.0Nov 2023View details →

Population Genomics Analysis of 30 Samples from Each of Multiple Populations Reveals Signatures of Selection from Breeding for Rapid Growth and Apical Dominance in Paulownia fortunei

Paulownia fortunei is an ecologically and economically valuable tree cultivated for its rapid growth and high-quality timber. To enhance Paulownia germplasm, we have developed the elite variety QingT with patented advantages in growth rate and apical dominance. To illuminate the genetic basis of QingT's superior traits, here we harness comparative population genomics to analyze genomic variation patterns between QingT and common Paulownia. We performed whole-genome re-sequencing of 30 QingT and 30 common samples, detecting 15.6 million SNPs and 2.6 million indels. Phylogeny and population structure analyses robustly partitioned common and QingT into distinct groups which indicate robust genome stabilization. QingT exhibited reduced heterozygosity and linkage disequilibrium decay compared to common Paulownia, reflecting high recombination, indicating hybridizing effects with common white-flowered string is the source of its patented advantages. Genome selection scans uncovered 25 regions of 169 genes with elevated nucleotide diversity, indicating selection sweeps among groups. Functional analysis of sweep genes revealed upregulation of ribosomal, biosynthesis and growth pathways in QingT, implicating enhanced protein production and developmental processes in its rapid growth phenotype. This study's insights comprehensively chart genomic variation during Paulownia breeding, localizing candidate loci governing agronomic traits, and underpinnings of future molecular breeding efforts to boost productivity.