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opencc-zeroOct 2021View details →

Temporary Allee effects among non-stationary recruitment dynamics in depleted gadid and flatfish populations

We investigated whether low-abundance recruitment dynamics can change in time between compensation and depensation, the latter implying the presence of the Allee effect. For this, we studied the stock-recruitment time series of 17 gadid and flatfish populations in the RAM Legacy Stock Assessment Database using a Bayesian change point model. The recruitment dynamics were represented with the sigmoidal Beverton-Holt and the Saila-Lorda stock-recruitment models, and the parameters of the models were allowed to shift at a priori unknown change points.

opencc-zeroDec 2021View details →

Data for Nicola Chinook Ricker stock-recruit model with environmental covariates

<ol> <li>Climate change and human activities are transforming river flows globally, with potentially large consequences for freshwater life. To help inform watershed and flow management, there is a need for empirical studies linking flows and fish productivity.</li> <li>We tested the effects of river conditions and other factors on 22 years of Chinook salmon productivity in a watershed in British Columbia, Canada.</li> <li>Freshwater conditions during adult salmon migration and spawning, as well as during juvenile rearing, explained a large amount of variation in productivity.</li> <li>August river flows while salmon fry reared had the strongest effect on productivity – our model predicted that cohorts that experience 50% below average flow in the August of rearing have 21% lower productivity.</li> <li>These contemporary relationships are set within long-term changes in climate, land use, and hydrology. Over the last century, average August river discharge decreased by 26%, air temperatures warmed, and water withdrawals increased. 17% of the watershed was logged in the last 20 years. </li> <li>Our results suggest that, in order to remain stable, this Chinook salmon population being assessed for legal protection requires substantially higher August flow than previously recommended. Changing flow regimes – driven by watershed impacts and climate change – can threaten imperiled fish populations.</li> </ol>

opencc-by-4.0Jan 2022View details →

Environment and density-dependency explain the fine-scale distribution of tree recruits before and after thinning

Dataset used in the article "Environment and density-dependency explain the fine-scale distribution of tree recruits before and after thinning" in PeerJ

opencc-by-4.0Mar 2022View details →

Seedling recruitment and sapling bank dynamics on fluvial deposits in a temperate montane riparian forest.

This is a dataset of Seedling recruitment and sapling bank dynamics on fluvial deposits in a temperate montane riparian forest. The followings are details of each file. Saplings_inFluvialDepositsv1.0.0.csv <ul> <li><code>Plot_x</code>    Factor. X coordinates of plots.</li> <li><code>Plot_y</code>    Factor. Y coordinates of plots.</li> <li><code>x</code>    Integer. X coordinates in plots.</li> <li><code>y</code>    Integer. Y coordinates in plots.</li> <li><code>Substrate</code>    Factor. Established substrates. NA means that it was not recorded.</li> <li><code>stemID</code>    Character. The ID of individual trees.</li> <li><code>Sp.</code>    Factor. The species names.</li> <li><code>Family</code>    Factor. The family name of the species.</li> <li><code>Heightyyyy</code>    Numeric. Vertical heights of trees (cm) in yyyy. Height2007ad is the heights after disturbance in 2007.</li> <li><code>Lengthyyyy</code>    Numeric. Length of trees (cm) in yyyy. Length2007ad is the length after disturbance in 2007.</li> <li><code>DBH1_yyyy</code>, <code>DBH2_yyyy</code>    Numeric. Diameter at breast height (mm) in yyyy. DBH1 and DBH2 were measured to cross at right angles.</li> <li><code>Noteyyyy</code>    Character. Comments in yyyy.</li> </ul>   Seedlings_inFluvialDepositsv1.0.0.csv <ul> <li><code>Plot</code>    Factor. The plot ID.</li> <li><code>ID</code>    Character. The individual ID.</li> <li><code>Sp.</code>    Factor. The species names.</li> <li><code>Family</code>    Factor. The family names of species.</li> <li><code>Hyyyy</code>    Numeric. Vertical height of trees (cm) in yyyy.</li> <li><code>Ageyyyy</code>    Numeric. The years of trees (cm) in yyyy.</li> <li><code>noteyyyy</code>    Character. Comment in yyyy.</li> </ul>   Map_FluvialDeposits.pdf <ul> <li><code>p. 1</code>: The overall picture of the positional relations between each gap.</li> <li><code>p. 2</code>: The details of seedling quadrats.</li> </ul>   Metadata_Saplings_inFluvialDeposits.txt Metadata of "Saplings_inFluvialDepositsv1.0.0.csv". It is the same as this description.   Seedlings_inFluvialDepositsv1.0.0.csv Metadata of "Seedlings_inFluvialDepositsv1.0.0.csv". It is the same as this description.

opencc-zeroDec 2021View details →

Using marsh organs to test seed recruitment in tidal freshwater marshes

Premise: Seed recruitment niches along estuarine elevation gradients are seldom experimentally field-tested under tidal regimes of the Pacific Northwest of North America. Addressing this knowledge gap is important to better understand estuary restoration and plant community response to sea level rise. Methods: Germination was tested in marsh organ mesocosms across an elevation gradient (0.5–1.7 m above mean sea level). Seeds were sown on sterile peat moss, and the tops of pipes were secured with horticultural "frost cloth" to ensure no experimental seeds were washed out and no new seeds were introduced. The trials tested artificial and overwinter chilling regimes, as well as the presence and/or absence of a near-neighbor transplant. Results: Carex lyngbyei had significant elevation-driven germination after overwinter and artificial chilling. Schoenoplectus tabernaemontani had near-significant germination across elevation after overwinter chilling, and germination in the absence of competition was significantly greater than with a near-neighbor transplant. Discussion: Carex lyngbyei had the highest germination rate at higher elevations, which suggests restricted seed recruitment potential, and required clonal expansion to extend into lower marsh elevations. Identifying species-specific recruitment niches provides insight for restoration opportunities or invasive species monitoring, as well as for estuary migration under sea level rise.

opencc-zeroJun 2022View details →

Different genes are recruited during convergent evolution of pregnancy and the placenta

The repeated evolution of the same traits in distantly related groups (convergent evolution) raises a key question in evolutionary biology: do the same genes underpin convergent phenotypes? Here, we explore one such trait, viviparity (live birth), which, qualitative studies suggest, may indeed have evolved via genetic convergence. There are 150 independent origins of live birth in vertebrates, providing a uniquely powerful system to test the mechanisms underpinning convergence in morphology, physiology, and/or gene recruitment during pregnancy. We compared transcriptomic data from eight vertebrates (lizards, mammals, sharks) that gestate embryos within the uterus. Since many previous studies detected qualitative similarities in gene use during independent origins of pregnancy, we expected to find significant overlap in gene use in viviparous taxa. However, we found no more overlap in uterine gene expression associated with viviparity than we would expect by chance alone. Each viviparous lineage exhibits the same core set of uterine physiological functions. Yet, contrary to prevailing assumptions about this trait, we find that none of the same genes are differentially expressed in all viviparous lineages, or even in all viviparous amniote lineages. Therefore, across distantly related vertebrates, different genes have been recruited to support the morphological and physiological changes required for successful pregnancy. We conclude that redundancies in gene function have enabled the repeated evolution of viviparity through recruitment of different genes from genomic "toolboxes", which are uniquely constrained by the ancestries of each lineage.

opencc-by-4.0Apr 2024View details →

Group-level trait and individual performance: the impact of in-nest activity on food recruitment in ants

Dataset, R and Python scripts corresponding to the results displayed in the article "Group-level trait and individual performance: the impact of in-nest activity on food recruitment in ants". R script works in pair with all three .csv files. .txt files are example of output generated by the Python script that analyses a worker's path inside the nest. 3 videos from the experiment are also available. They allow visualization of the setup as well as testing of Python scripts.

opencc-zeroMay 2024View details →

Data from: Climatic disequilibrium of recruit communities across a drought-induced die-off gradient in Mediterranean shrubland

Positive plant–plant interactions (facilitation) may enhance the recruitment and establishment of species less adapted to local macroclimatic conditions. A major cause of this effect is climatic buffering, which implies an increased mismatch between the macroclimatic conditions and the climatic requirements of the existing community – climatic disequilibrium – of plants living under canopies. Here we explore the effect of drought-induced defoliation of Mediterranean shrubland canopy on the recruitment of woody species. We analyzed the differences in the climatic disequilibrium across different categories of canopy defoliation and plant–plant interactions: facilitation, neutral and inhibition. Climatic disequilibrium was estimated as the Euclidean distance in the multivariate environmental space between observed macroclimate and community inferred climate. The inferred climate was calculated by averaging the coordinates of the species' climatic niche centroids, obtained from species distribution, weighted by the species' relative abundances in each community. We found that the recruiting community growing under canopy showed higher climatic disequilibrium than the community growing in the gaps. The facilitated recruiting community growing under dead and living canopy showed the highest disequilibrium, followed by the community growing under mid-affected canopy. The climatic disequilibrium of the recruiting communities experiencing neutral and inhibited interaction was not affected by canopy defoliation. These findings indicate that the climatic disequilibrium of the recruiting community is determined by the facilitation–competition balance. Living canopy provides climatic buffering, but it also implies competition, while dead canopy may provide some structural climatic buffering, without implying competition for resources. These results highlight the relevance of incorporating plant–plant interactions, particularly facilitation, to better forecast plant community responses to extreme climate events and climate change.

opencc-zeroJun 2024View details →

Negative parental and offspring environmental effects of macroalgae on coral recruitment are linked with alterations in the coral larval microbiome

The persistence of reef-building corals is threatened by macroalgal competitors leading to a major demographic bottleneck in coral recruitment. Whether parental effects exist under coral-algal competition and whether they influence offspring performance via microbiome alterations represent major gaps in our understanding of the mechanisms by which macroalgae may hinder coral recovery. We investigated the diversity, variability and composition of the microbiome of adults and larvae of the coral Pocillopora acuta and surrounding benthic substrate on algal-removed and algal-dominated bommies. We then assessed the relative influence of parental and offspring environmental effects on coral recruitment processes by reciprocally exposing coral larvae from two parental origins (algal-removed and algal-dominated bommies) to algal-removed and algal-dominated environmental conditions. Dense macroalgal assemblages impacted the microbiome composition of coral larvae. Larvae produced by parents from algal-dominated bommies were depleted in putative beneficial bacteria and enriched in opportunistic taxa. These larvae had a significantly lower survival compared to larvae from algal-removed bommies regardless of environmental conditions. In contrast, algal-induced parental and offspring environmental effects interacted to reduce the survival of coral recruits. Together our results demonstrate negative algal-induced parental and offspring environmental effects on coral recruitment that could be mediated by alterations in the offspring microbiome.

opencc-by-4.0Feb 2024View details →

Connectivity modelling identifies sources and sinks of coral recruitment within reef clusters

This study uses biophysical modelling to estimate coral larval connectivity estimates within the Moore Reef cluster, northern Great Barrier Reef, for the annual spawning events of Acropora corals in 2015, 2016 and 2017. Moore_2015_simple.nc, Moore_2016_simple.nc and Moore_2017_simple.nc contain the hydrodynamic data for the Moore Reef cluster. Moore_grid.nc contains the Moore Reef cluster grids data and Moore_spatial.csv contain the centroids of spatial polygons in the Moore Reef cluster. sysdata.rda contains GBR1 grids data, u_spring.rds and u_gbr1.rds contain mean surface velocities for Moore Reef cluster and GBR1 domain. The transfer probability matrix data contain the connectivity matrices for the days and years that were considered.

opencc-by-4.0Dec 2022View details →

Fig 2 in Bivalve Spat (Anadara granosa) recruitment in rehabilitation mangrove ecosystem of Rangsang Island, Riau province

Fig 2: Distribution of Mangrove Density in the Mangrove Ecosystem Rehabilitation of Rangsang Island, Riau

opencc-zeroJun 2024View details →

Wood duck nest survival and duckling recruitment is minimally affected by interspecific brood parasitism from hooded mergansers and black-bellied whistling-ducks

In the southeastern United States, wood ducks (Aix sponsa) have historically experienced interspecific brood parasitism (IBP) primarily from hooded mergansers (Lophodytes cucullatus), but the recent northward expansion of black-bellied whistling-ducks (Dendrocygna autumnalis) has added a new complexity to these interactions. We monitored nest boxes in Louisiana to evaluate the influence IBP had on wood duck daily nest survival rate (after, DSR) and duckling recruitment. We monitored 1,295 wood duck nests from 2020−2023 and found 112 (8.7%) were parasitized by hooded mergansers and 148 (11.5%) by whistling-ducks. Parasitic egg-laying by hooded mergansers lowered wood duck DSR, while DSR for nests parasitized by whistling-ducks was comparable to clutches containing only wood duck eggs. We considered the wood duck capture histories of 2,465 marked female ducklings and 540 banded adult females to estimate a duckling recruitment probability for the entire study period. We recaptured 50 ducklings as adults; 6 (12.0%) hatched from clutches parasitized by hooded mergansers, 1 (2.0%) from a clutch parasitized by a whistling-duck, and 43 (86.0%) from clutches containing only wood duck eggs. The duckling recruitment probability was 0.039 (95% credible interval = 0.028, 0.051). Nest initiation date had a negative effect on recruitment, wherein most recruits hatched from nests initiated earlier in the season. Given only ~9% of wood duck nests contained hooded merganser eggs, we conclude IBP writ large had no detrimental effect on DSR at a population level. The lower DSR of clutches parasitized by hooded mergansers is potentially linked to a high abundance of early-season parasites that produce "dump nests" and these clutches are often abandoned without being incubated. Despite ongoing parasitism by hooded mergansers and the range expansion of whistling-ducks, wood duck productivity in Louisiana appears to be minimally affected by interspecific brood parasitism.

opencc-by-4.0Dec 2022View details →

Fig 4 in Bivalve Spat (Anadara granosa) recruitment in rehabilitation mangrove ecosystem of Rangsang Island, Riau province

Fig 4: Relationship between Spat Abundance of Bivalve A. granosa and Mangrove Density in Rangsang Island, Riau (A) November 2020 (B) December 2020 (C) January 2021

Figure 6 in Recruitment biology of cleavers (GOlium spp.) populations in western Canada

Figure 6. Emergence percentage of Canadian Galium spp. populations in fall of (A) 2013 and (B) 2014. Error bars represent SE, and similar letters indicate values do not differ statistically at P = 0.05. SPG, Saskatchewan Pulse Growers.

Figure 4 in Recruitment biology of cleavers (GOlium spp.) populations in western Canada

Figure 4. Cumulative emergence percentage of Canadian Galium spp. populations in spring of (A) 2013 and (B) 2014. Error bars represent SE, and similar letters indicate values do not differ statistically at P = 0.05. SPG, Saskatchewan Pulse Growers.

Figure 5 in Recruitment biology of cleavers (GOlium spp.) populations in western Canada

Figure 5. Emergence timing of Galium spp. populations (observed and predicted values, respectively) at Goodale in the fall of (A) 2013 and (B) 2014. Growing degree days (GDD) were determined with a base temperature of 2 C. Arrows indicate significant rainfall events (16.2 mm at 600 GDD in 2013 and 4.8 mm and 7.8 mm at 150 and 360 GDD in 2014).SPG, Saskatchewan Pulse Growers.

Figure 3 in Recruitment biology of cleavers (GOlium spp.) populations in western Canada

Figure 3. Emergence timing of Galium spp. at Goodale in the spring of 2013 (left) and 2014 (right). Growing degree days (GDD) were determined with a base temperature of 2 C. Arrows indicate significant rainfall events (8.4 and 47 mm in 2013 at 200 and 350 GDD, and 51 and 63 mm in 2014 at 200 and 400 GDD, respectively). SPG, Saskatchewan Pulse Growers.

Figure 2 in Recruitment biology of cleavers (GOlium spp.) populations in western Canada

Figure 2. The effect of temperature on percent germination of Galium spp. populations from different locations on the Canadian Prairies.Data points represent the means of two trial runs conducted using the thermogradient plate. SPG, Saskatchewan Pulse Growers.

Figure 1 in Recruitment biology of cleavers (GOlium spp.) populations in western Canada

Figure 1. Google map showing Saskatchewan and Alberta locations where Galium spp. populations were collected.