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opencc-by-4.0Nov 2023View details →

Effects of Salinity on the Reproductive Cycle of the Mangrove Oyster Crassostrea tulipa in Hatchery Conditions

Aim: Development of hatchery techniques for Crassostrea gasar seed supplies, including animal conditioning using salinity manipulation.A protocol for conditioning using salinity manipulation for C. gasar was developed based on review of existing literature and data from previous projects. The protocol was tested and evaluated by university partners in southern Brazil, refined by Embrapa and then transferred to industry partners.

opencc-by-4.0Sep 2023View details →

Reproduction dataset for EcoScape analysis

This dataset facilitates the reproduction of the initial paper on EcoScape.In this version of the dataset, we have included also the Omniscape input and output, to facilitate the reproduction of the comparison.

opencc-by-4.0Dec 2023View details →

Intensive male competition caused severity of trauma in female genital tracts predicts female reproductive success and longevity in strictly monandrous wolf spiders

This is the raw data for the manuscript of Dr. Shichang Zhang from Hubei University entitled: Intensive male competition caused severity of trauma in female genital tracts predicts female reproductive success and longevity in strictly monandrous wolf spiders.

Reproductive state alters vocal characteristics of female North American red squirrels (Tamiasciurus hudsonicus)

Female advertisement of reproductive state and receptivity has the potential to play a large role in the mating systems of many taxa, but investigations of this phenomenon are underrepresented in the literature. North American red squirrels (Tamiasciurus hudsonicus) are highly territorial and engage in scramble competition mating, with males converging from spatially disparate territories to engage in mating chases. Given the narrow estrus window exhibited in this species, the ubiquitous use of vocalizations to advertise territory ownership, and the high synchronicity of males arriving from distant territories, we hypothesized that female vocalizations contain cues relating to their estrous state. To test this hypothesis, we examined the spectral and temporal properties of female territorial rattle vocalizations collected from females of known reproductive condition over 3 years. While we found no distinct changes associated with estrus specifically, we did identify significant changes in the spectral characteristics of rattles relating to both female body mass and reproductive state relative to parturition. To the best of our knowledge, this is the first evidence of changes in vocal characteristics associated with late pregnancy in a non-human mammal.

Figure 5 in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Figure 5. – Development of Z. asper before hatching. A: Embryo at 4 days; B: Embryo at 12 days; C: Hatching at 20 days.

Figure 6 in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Figure 6. – Development of Z. asper after hatching. A: Larvae post-hatching; B: Pelagic larvae at 5 days; C: Benthic phase at 15 days; D: Juvenile phase at 40 days.

Figure 10 in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Figure 10. – Annual thermal cycle for different life phases of Z. asper. The "gametogenesis" phase starts when temperatures fall in September and continues throughout the winter but slows down in November when the temperature reaches 5°C. This period of time at 5°C, indicated as "vernalization" on the graph, lasts from November to February. The duration of this period is very important because it directly conditions the success of the reproduction. Rapid and regular rising of temperatures to 10°C triggers reproduction from the beginning of March and continues until the end of April.

Figure 3. – A in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Figure 3. – A: Growth curve of the Z. asper group born in captivity (2008) descended from wild Z. asper from the Beaume. At 2 years old, some fish could not be sexed but all Z. asper were mature at 3 years and monitoring of both sexes was possible. At 5 years old, females are significantly longer than males. B: Quantity of food per week for 20 asper (Beaume 2008) in 2015. When the temperature reaches 14 to 15°C in May, Z. asper consume 3 times the quantity of food eaten at 5 to 10°C. From 20°C in July, consumption levels are more than 5 times higher than in the winter.

Figure 9. – A in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum

Figure 9. – A: Comparison of incubation results as a function of cold period length from 30 to 120 days. More than 64,000 eggs were collected during these trials and all egg clutches were accurately counted at four key moments of the incubation process: on laying, at 10 days, at transfer for hatching and at hatching. From the first development stages, egg mortality declines as the length of the winter cold period increases. B: Clutch by clutch detail of the incubation survival rate of eggs for batches of "Beaume" broodstock subjected to 3 different temperature periods. The egg clutches produced during the same experiment are identified by an identical colour. Within the same group, survival rate results sometimes varied widely. The hatching rates for broodstock subjected to 90 days of vernalization are the most variable. This wide variability suggests that the 90-day period of cold temperatures creates a boundary, which determines whether reproduction is successful or not. C: Variation in hatching rate (mean and standard deviation) as a function of vernalization period length. Unlike those from the "Beaume" stock, Z. asper of "Durance" stock we used in 2016 and 2017 (captured in 2015 and 2016), were replaced between the two years. The hatching rate varies in accordance with the duration of the cold period experienced by the broodstock during the winter. For the "Beaume" broodstock, Kruskal-Wallis tests show that comparisons between the results obtained with the 120-day period and the other periods are significant (p <0.05). The length of the vernalization period clearly has an influence on the hatching rate. This test was also applied to data from the experiments involving both sets of stock and 120-day periods. As this test was not significant (p = 0.07), it demonstrates that both sets of stock reacted similarly to this vernalization period.

Low sex drive and choosy females: Fungal infections are a reproductive downfall for male house flies

Many entomopathogenic fungi cause infections that kill their insect host. Little is understood about changes in the reproductive investment that occur during an infection by a lethal disease over the waning life of an insect. Life history theory suggests the host will respond by investing resources into fighting the disease or increasing reproduction. Here, we investigate how the reproductive life of adult house flies, Musca domestica, is impacted by its host-specific fungal pathogen, Entomophthora muscae. Specifically, we test how the week-long infection alters the mating behavior of virgin adult male house flies. We find that the pathogen significantly decreases male libido; an effect which grows stronger over the course of the infection. Furthermore, females were significantly less likely to choose an infected male, reducing male mating success. Additionally, we assessed sperm viability to understand the reproductive costs for monandrous females to mate with infected males. Analyses revealed that sperm quality decreases as early as three days post-infection. These results show that E. muscae, which can have a prevalence near 100% in wild populations, causes severe lifetime reproductive costs to male house flies. Understanding how host-pathogen interactions affect host life history is crucial for elucidating all the negative effects pathogen virulence exerts on hosts.

Divergence in reproductive behaviors is associated with the evolutionary loss of parental care

The mechanisms underlying the divergence of reproductive strategies between closely-related species are still poorly understood. Additionally, it is unclear which selective factors drive the evolution of reproductive behavioral variation and how these traits coevolve, particularly during early divergence. To address these questions, we quantified behavioral differences in a recently diverged pair of Nova Scotian three-spined stickleback (Gasterosteus aculeatus) populations, which vary in parental care, with one population displaying paternal care and the other lacking this. We compared both populations, and a full reciprocal F1 hybrid cross, across four major reproductive stages: territoriality, nesting, courtship, and parenting. We identified significant divergence in a suite of heritable behaviors. Importantly, F1 hybrids exhibited a mix of behavioral patterns, some of which suggest sex-linkage. This system offers fresh insights into the coevolutionary dynamics of reproductive behaviors during early divergence and offers support for the hypothesis that coevolutionary feedback between sexual selection and parental care can drive rapid evolution of reproductive strategies.

Food and social cues modulate reproductive development but not migratory behavior in a nomadic songbird, the Pine Siskin (Pinus spinus)

Many animals rely on photoperiodic and non-photoperiodic environmental cues to gather information and appropriately time life history stages across the annual cycle, such as reproduction, molt, and migration. Here, we experimentally demonstrate that the reproductive physiology, but not migratory behavior, of captive Pine Siskins responds to both food and social cues during the spring migratory-breeding period. Pine Siskins are a nomadic finch with a highly flexible breeding schedule and, in the spring, free-living Pine Siskins can wander large geographic areas and opportunistically breed. To understand the importance of non-photoperiodic cues to the migratory-breeding transition, we maintained individually housed birds on either a standard or enriched diet in the presence of group-housed heterospecifics or conspecifics experiencing either the standard or enriched diet type. We measured body condition and reproductive development of all Pine Siskins and, among individually housed Pine Siskins, quantified nocturnal migratory restlessness. In group-housed birds, the enriched diet caused increases in body condition and, among females, promoted reproductive development. Among individually housed birds, female reproductive development differed between treatment groups whereas male reproductive development did not. Specifically, individually housed females showed greater reproductive development when presented with conspecifics compared to heterospecifics. The highest rate of female reproductive development, however, was observed amongst individually housed females provided the enriched diet and maintained with group-housed conspecifics on an enriched diet. Changes in nocturnal migratory restlessness did not vary by treatment group or sex. By manipulating both the physical and social environment, this study demonstrates how multiple environmental cues can affect the timing of transitions between life history stages with differential responses between sexes and between migratory and reproductive systems.

Relative breeding timing and reproductive success of a resident montane bird species

The phenological match-mismatch hypothesis predicts that animals that better synchronize critical life history events with the peak availability of their primary food source should have higher fitness. If phenological match-mismatch determines breeding success, most individuals in a population may be expected to breed simultaneously within a given year because selection has favored mechanisms that allow for the tracking of optimal food abundance. Therefore, individuals that breed too early or too late relative to the bulk of the population ("peak" of breeding) should experience decreased fitness. Using 11 years of data, we investigated the effect of relative breeding timing on breeding success in resident mountain chickadees (Poecile gambeli) across two elevations in the Sierra Nevada mountains, USA. Chickadees that bred during the peak of nesting did not have the highest breeding success; instead, birds that bred earliest performed best at high elevation, while at low elevation early and peak nests performed similarly. Breeding success decreased linearly with relative timing at both high and low elevations, and the relationship between breeding success and timing differed among years. Our results suggest that phenological match-mismatch may not be the main driver of within-year variation in breeding success in animals residing in montane environments.

opencc-by-4.0Jan 2024View details →

Linking diet switching to reproductive performance across populations of two Critically Endangered mammalian herbivores

Data associated with Harvey Sky, N., Britnell, J., Antwis, R. et al. Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores. Commun Biol 7, 333 (2024). https://doi.org/10.1038/s42003-024-05983-3 The data deposited here includes raw metabarcoding output fasta files and some processed metabarcoding and sample data in xslx files. We include a more detailed description of each file below. Data regarding Kenyan black rhino and Grevy’s zebra are treated as sensitive and confidential. There are therefore restrictions on the data that we can make available. Due to these confidentiality considerations, the sample data stored here does not include locations of sample collection within each reserve for either species, or the identity or breeding data for black rhino. It also only includes the final processed values for NDVI and rainfall. The remote sensing data is available from the repositories cited in the methods, but we cannot provide the shapefiles or other data used to calculate the final values for each sample.  Raw fasta files_plants.zip A zipped folder containing the raw fasta files which were the output from the MiSeq sequencing of dietary plants in the faecal samples for both black rhino and Grevy's zebra. Within the zipped folder, the first part of the title of each fasta.gz file is the sample code (S1, S2, S3 etc), which allows you to cross reference these files with the sample data and processed sequencing data in the xslx files. Files with R1 in the title are foward reads, and R2 are reverse reads.  Raw fasta files_bacteria.zip A zipped folder containing the raw fasta files which were the output from the MiSeq sequencing of microbiome bateria in the faecal samples for both black rhino and Grevy's zebra. Within the zipped folder, the first part of the title of each fasta.gz file is the sample code (S1, S2, S3 etc), which allows you to cross reference these files with the sample data and processed sequencing data in the xslx files. Files with R1 in the title are foward reads, and R2 are reverse reads.  Sample data and processed metabarcoding data_Black rhino.xlsx Sample data tab The data that we are able to share that is associated with each black rhino sample. SampleID - The code used to identiy each sample which allows it be cross-referenced with other tabs and the fasta files.  IndividualID - We are not able to share rhino names or other identifiers, but we have given each individual a unique number so that it can be seen which samples came from the same individuals.  NDVI - Mean NDVI of each individual's area of utilisation in the 10-day period  within which the sample was collected. The method used to calculate this is described in the methods of the article.  Rainfall - Cumulative rainfall over the 30 days previous to sample collection for the 0.05 degree pixel under the sample. The method used to calculate this is described in the methods of the article.  Season - Post is the post-rain sampling season June-July 2018. Pre is the pre-rain sampling season January-March 2019.  Reserve - The reserve that the sample was collected on.  Date - The date of sample collection.  Dietary breadth - Shannon-Wiener index of dietary alpha diversity. The method used to calculate this is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding. Poaceae, Fabaceae, Ebenaceae - The relative abundance of each of these three dietary plant families that were the focus of our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding. Bacteria numbers of reads The number of reads assigned to each bacterial ASV found in each sample.  Bacteria sequences and reads The sequence of each ASV, and the taxa assigned to each sequence in the microbiome metabarcoding. The method for taxonomic assignment is described in the methods of the article.  Plant numbers of reads The number of reads assigned to each dietary plant ASV found in each sample.  Plant sequences and reads The sequence of each ASV, and the taxa assigned to each sequence in the dietary plant metabarcoding. The method for taxonomic assignment is described in the methods of the article.    Sample data and processed metabarcoding data_Grevy's zebra.xlsx Sample data tab The data that we are able to share that is associated with each Grevy's zebra sample. Sample ID - The code used to identiy each sample which allows it be cross-referenced with other tabs and the fasta files.  NDVI - Mean NDVI of each individual's area of utilisation in the 10-day period  within which the sample was collected. The method used to calculate this is described in the methods of the article.  Rainfall - Cumulative rainfall over the 30 days previous to sample collection for the 0.05 degree pixel under the sample. The method used to calculate this is described in the methods of the article.  Reserve - The reserve that the sample was collected on.  Season - Post is the post-rain sampling season July-August 2018. Pre is the pre-rain sampling season January-February 2019.  Date - The date of sample collection.  Dietary breadth - Shannon-Wiener index of dietary alpha diversity. The method used to calculate this is described in the methods of the article.  Poaceae, Fabaceae - The relative abundance of each of these two dietary plant families that were the focus of our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding. Indigofera - The relative abundance of each of this Fabaceae genus was included in our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding. Bacteria numbers of reads The number of reads assigned to each bacterial ASV found in each sample.  Bacteria sequences and reads The sequence of each ASV, and the taxa assigned to each sequence in the microbiome metabarcoding. The method for taxonomic assignment is described in the methods of the article.   Plant numbers of reads The number of reads assigned to each dietary plant ASV found in each sample.  Plant sequences and reads The sequence of each ASV, and the taxa assigned to each sequence in the dietary plant metabarcoding. The method for taxonomic assignment is described in the methods of the article.

Energetic trade-offs in migration decision-making, reproductive effort, and subsequent parental care in a long-distance migratory bird

Migratory species trade-off long-distance movement with survival and reproduction, but the spatiotemporal scales at which these decisions occur is relatively unknown. Technological and statistical advances allow fine-scale study of animal decision-making, improving our understanding of possible causes and therefore conservation management. We quantified effects of reproductive preparation during spring migration on subsequent breeding outcomes, breeding outcomes on autumn migration characteristics, and autumn migration characteristics on subsequent parental survival in Greenland white-fronted geese (Anser albifrons flavirostris). These are long-distance migratory birds with a ~50% population decline from 1999 to 2022. We deployed GPS-acceleration devices on adult females to quantify up to five years of individual decision-making throughout the annual cycle. Weather and habitat-use affected time spent feeding and overall dynamic body acceleration (i.e., energy expenditure) during spring and autumn. Geese that expended less energy and fed longer during spring were more likely to successfully reproduce. Geese with offspring expended more energy and fed for less time during autumn, potentially representing adverse fitness consequences of breeding. These behavioural comparisons among Greenland white-fronted geese improve our understanding of fitness trade-offs underlying abundance. We provide a reproducible framework for full annual cycle modelling using location and behaviour data, applicable to similarly studied migratory animals.

Reproductive success of hatchery- and natural-spawning sockeye salmon, Auke Creek, Alaska

Evaluating salmon hatchery supplementation programs requires assessing not only program objectives but identifying potential risks to wild populations as well. Such evaluations can be hampered by difficulty in distinguishing between hatchery- and wild-born returning adults. Here, we conducted three years (2011–2013) of experimental hatchery supplementation of sockeye salmon in Auke Lake, Juneau, Alaska where a permanent weir allows sampling and genotyping of every returning adult (2008–2019). We identified both hatchery- and wild-born returning adults with parentage assignment, quantified the productivity (adult offspring/spawner) of hatchery spawners relative to that of wild spawners, and compared run timing, age, and size at age between hatchery- and wild-born adults. Hatchery-spawning females produced approximately six to 50 times more returning adults than did naturally spawning females. Supplementation had no discernable effect on run timing and limited consequences for size at age, but we observed a distinct shift to younger age at maturity in the hatchery-born individuals in all three brood years. The shift appeared to be driven by hatchery-born fish being more likely to emigrate after one, rather than two, years in the lake but the cause is unknown. In cases when spawning or incubation habitat is limiting sockeye salmon production, hatchery supplementation can be effective for enhancing the number of returning adult fish but not without the risk of phenotypic change in the recipient population, which can be an undesired outcome of hatchery supplementation. This study adds to a growing body of evidence suggesting that phenotypic change within a single generation of captive spawning might be widespread in salmon hatchery programs.

opencc-by-4.0Nov 2023View details →

Climate warming and temporal variation in reproduction strategies in the endangered meadow viper

Here, we used more than three decades of mark-recapture data in a natural population of the endangered meadow viper (Vipera ursinii ursinii) to unravel the patterns of temporal variation in reproductive traits, local climatic determinants of inter-annual variation in reproduction and the potential buffering effects of life cycle on population growth rate. We found significant inter-annual variation in annual body growth, gestation length, post-parturition body condition, clutch success and offspring traits at birth, but little temporal effects in reproductive effort. Temperature during gestation was the most influential local climatic determinant by shortening gestation length, and increasing clutch success and post-parturition body condition. Neither air humidity nor insolation was found to influence reproduction.

opencc-by-4.0Feb 2024View details →

An unusual pulse shape change event in PSR J1713+0747 observed with the Green Bank Telescope and CHIME: Profile data and figure reproduction scripts

This Zenodo entry contains data used in the paper "An unusual pulse shape change event in PSR J1713+0747 observed with the Green Bank Telescope and CHIME", to be published in The Astrophysical Journal. This includes minimally processed profile data in PSRFITS format, as well as pulsar ephemerides (.par files), time-of-arrival estimates (.tim files), and scripts which can be used to reproduce the figures and tables in the paper. For more information, see README.md.

opencc-zeroFeb 2024View details →

The reproductive microbiome and maternal transmission via eggs in Sceloporus virgatus

Maternal transmission of microbes occurs across the animal kingdom and is vital for the development and long-term health of offspring. The mechanisms of this transfer are most well studied in humans and other mammals, but are less well understood in egg-laying animals, especially in those with no parental care. Here we investigate the transfer of maternal microbes in Sceloporus virgatus, an oviparous spiny lizard. We compared three maternal tissue microbiomes – oviduct, cloaca, and intestine – to three offspring sample types: egg contents and eggshells on the day of oviposition, and hatchling intestinal tissue on the day of hatching. We found that dam ID is an important factor in hatchling microbiome composition, indicating that maternal transmission is occurring. The maternal cloacal and oviductal communities contribute to offspring microbiomes in all three sample types, but there was minimal influence of maternal intestinal microbes. This indicates that the maternal reproductive microbiome is more important for microbial inheritance than the gut microbiome, and that the tissue-level variation of the adult S. virgatus microbiome must develop as the hatchling matures. Despite differences between adult and hatchling communities, the offspring microbiome was still dominated by Enterobacteriaceae and Yersiniaceae, consistent with past studies of adult S. virgatus microbiomes.