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opencc-zeroJan 2024View details →

Data for: Effective population size mediates the impact of pollination services on pollen limitation

Inadequate pollen receipt limits flowering plant reproduction worldwide. Ecological causes of pollen limitation ('PL'), like pollinator scarcity and low plant abundance, have been a primary focus of research. The genetic diversity of plant populations could impact both quantity and quality components of PL in concert with ecological factors, yet empirical examples are lacking. We evaluated joint effects of ecological factors (flower abundance, pollinator visitation) and genetic effective population size (NE) on PL across 13 populations of a common herb. We used a histological approach with 5504 styles from 1137 flowers to separate quantity and quality components of PL, and link these to reproductive output. NE and pollinator visitation interacted to shape PL, but NE had stronger direct effects. Effectively smaller populations experienced stronger quantity PL, and controlled crosses in a pollinator-free environment revealed that pollen quantity was an intrinsic population-level attribute that increased with NE. Pollinator visitation enhanced pollen quality, but only in effectively larger populations. Quantity and quality PL negatively impacted fruit and seed set, respectively. Results highlight that PL is dictated by plant population genetic diversity in addition to commonly evaluated ecological factors. Efforts to support pollinators will only enhance plant reproduction in genetically diverse plant populations.

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.

Population size differences can lead to biases in phylogenetic inference and introgression detection in the presence of purifying selection

Phylogenetic reconstruction and introgression detection rely on an assumption about the probability distribution of gene tree topologies. Recently, evidence has emerged that population size differences can affect the probability distribution of gene tree topologies in the presence of purifying selection. Here, using the population genetic simulator SLiM, we provide evidence that in the presence of purifying selection, population size differences can lead to biases in phylogenetic inference. We also provide evidence that in the presence of purifying selection, population size differences can cause statistics used for introgression detection to exhibit patterns resembling those caused by introgression. In addition, we present a theoretical analysis showing that the occurrence of population size–dependent gene tree distributions is an inherent consequence of purifying selection. Our work underscores the importance of considering the potential confounding effect of purifying selection on phylogenetic inference and introgression detection.

Data and R code used in: Plant geographic distribution influences chemical defenses in native and introduced Plantago lanceolata populations

Plants growing outside their native range may be confronted by new regimes of herbivory, but how this affects plant chemical defense profiles has rarely been studied. Using Plantago lanceolata as a model species, we investigated whether introduced populations show significant differences from native populations in several growth and chemical defense traits. Plantago lanceolata (ribwort plantain) is an herbaceous plant species native to Europe and Western Asia that has been introduced to numerous countries worldwide. We sampled seeds from nine native and ten introduced populations that covered a broad geographic and environmental range and performed a common garden experiment in a greenhouse, in which we infested half of the plants in each population with caterpillars of the generalist herbivore Spodoptera littoralis. We then measured size-related and resource-allocation traits as well as the levels of constitutive and induced chemical defense compounds in roots and shoots of P. lanceolata. When we considered the environmental characteristics of the site of origin, our results revealed that populations from introduced ranges were characterized by an increase of chemical defense compounds without compromising plant biomass. The concentrations of iridoid glycosides and verbascoside, the major anti-herbivore defense compounds of P. lanceolata, were higher in introduced populations than in native populations. In addition, introduced populations exhibited greater rates of herbivore-induced volatile organic compound emission and diversity, and similar chemical diversity based on untargeted analyses of leaf methanol extracts. In general, the geographic origin of the populations had a significant influence on morphological and chemical plant traits, suggesting that P. lanceolata populations are not only adapted to different environments in their native range but also in their introduced range.

Global analysis of emperor penguin populations

Like many polar animals, emperor penguin populations are challenging to monitor because of the species' life history and remoteness. Consequently, it has been difficult to establish its global status, a subject important to resolve as polar environments change. To advance our understanding of emperor penguins, we combined remote sensing, validation surveys, and using Bayesian modeling we estimated a comprehensive population trajectory over a recent 10-year period, encompassing the entirety of the species' range. Reported as indices of abundance, our study indicates with 81% probability that the global population of adult emperor penguins declined between 2009 and 2018, with a posterior median decrease of 9.6% (95% credible interval (CI) -26.4% to +9.4%). The global population trend was -1.3% per year over this period (95% CI = -3.3% to +1.0%) and declines likely occurred in four of eight fast ice regions, irrespective of habitat conditions. Thus far, explanations have yet to be identified regarding trends, especially as we observed an apparent population up-tick toward the end of time series. Our work potentially establishes a framework for monitoring other Antarctic coastal species detectable by satellite, while promoting a need for research to better understand factors driving biotic changes in the Southern Ocean ecosystem.

Effects of food supplementation and helminth removal on space use and spatial overlap in wild bank vole populations

Animal space use and spatial overlap can have important consequences for population-level processes such as social interactions and pathogen transmission. Identifying how environmental variability and inter-individual variation affect spatial patterns and in turn influence interactions in animal populations is a priority for the study of animal behavior and disease ecology. Environmental food availability and macroparasite infection are common drivers of variation, but there are few experimental studies investigating how they affect spatial patterns of wildlife. Bank voles (Clethrionomys glareolus) are a tractable study system to investigate spatial patterns of wildlife and are amenable to experimental manipulations. We conducted a replicated, factorial field experiment in which we provided supplementary food and removed helminths in vole populations in natural forest habitats and monitored vole space use and spatial overlap using capture-mark-recapture methods. Using network analysis, we quantified vole space use and spatial overlap. We compared the effects of food supplementation and helminth removal and investigated the impact of season, sex, and reproductive status on space use and spatial overlap. We found that food supplementation decreased vole space use while helminth removal increased space use. Space use also varied by sex, reproductive status, and season. Spatial overlap was similar between treatments despite up to three-fold differences in population size. By quantifying the spatial effects of food availability and macroparasite infection on wildlife populations, we demonstrate the potential for space use and population density to trade off and maintain consistent spatial overlap in wildlife populations. This has important implications for spatial processes in wildlife including pathogen transmission.

opencc-zeroMar 2024View details →

Data and code for: Nonlinear life table response analysis: Decomposing nonlinear and nonadditive population growth responses to changes in environmental drivers

Life table response experiments (LTREs) decompose differences in population growth rate between environments into separate contributions from each underlying demographic rate. However, most LTRE analyses make the unrealistic assumption that the relationships between demographic rates and environmental drivers are linear and independent, which may result in diminished accuracy when these assumptions are violated. In this study, we compare the relative efficacy of linear and second-order LTRE analyses in capturing changes in population growth rate caused by environmental driver changes. To explore this question, we analyze demographic data collected for three long-lived plant species: Ardisia escallonioides (Pascarella & Horvitz, 1998), Silene acaulis, and Bistorta vivipara (Doak & Morris, 2010). This repository includes data files containing vital rate (survival, growth, reproduction) observations or models for our three case studies, as well as an R script in which we use these demographic data to calculate linear and second-order LTRE approximations of changes in population growth rate for each system and generate the figures we present in our paper.

Fig. 2 in Phylogeography Of The Western Populations Of Stylodipus Telum (Rodentia, Dipodidae) Based On Mitochondrial Dna

Fig. 2. Phylogeographic reconstruction of S. telum based on cytb. BI posterior probability / ML bootstrap support per 1000 replications is indicated at the nodes (only values over 70 % are shown). Photo: S. telum falzfeini from Sagi (Oleshki District) by M. Rusin, 2017-05-17.

Fig. 1 in Phylogeography Of The Western Populations Of Stylodipus Telum (Rodentia, Dipodidae) Based On Mitochondrial Dna

Fig. 1. Sampling localities of S. telum used in the study. White — range of S. telum falzfeini (original unpublished data) and green — range of S. telum turovi (Shenbrot et al., 1995).

opencc-by-4.0Nov 2013View details →

Figs 2, 3 in Seasonal variations in ixodid tick populations on a commercial game farm in the Limpopo Province, South Africa

Figs 2, 3. Numbers of Rhipicephalus (Boophilus) decoloratus collected in wetter and drier months (2), and in warmer and cooler months (3).

opencc-by-4.0Oct 2023View details →

Fig. 3 in Report of a Feather Mite Species (Acariformes: Astigmata) from the Oriental White Stork, Ciconia boyciana (Ciconiiformes: Ciconiidae), Belonging to the Japanese Native Population

Fig. 3. Pelargolichus orientalis, male (A) and female (B). A, right setae se and si on prodorsal shield, dorsal view; B, posterior part of hysterosoma, dorsal view. Scale bars: 10 µm.

opencc-by-4.0Oct 2023View details →

Fig. 1 in Report of a Feather Mite Species (Acariformes: Astigmata) from the Oriental White Stork, Ciconia boyciana (Ciconiiformes: Ciconiidae), Belonging to the Japanese Native Population

Fig. 1. The taxidermy specimen of the Oriental White Stork Ciconia boyciana sampled in Toyooka City, Hyogo Prefecture, Japan.

Fig. 4 in Fluctuating Asymmetry And Length-Weight Relationship Of The Three Populations Of Sardinella Lemuru (Clupeiformes, Dorosomatidae) From Surigao Del Norte, Philippines

Fig. 4. Principal components (PC) inferred deformation grid and histogram of individual (symmetry) in Surigao City, Surigao del Norte.

Fig. 2 in Fluctuating Asymmetry And Length-Weight Relationship Of The Three Populations Of Sardinella Lemuru (Clupeiformes, Dorosomatidae) From Surigao Del Norte, Philippines

Fig. 2. Principal components (PC) inferred deformation grid and histogram of individual (symmetry) in Malimono, Surigao del Norte.

Fig. 1 in Fluctuating Asymmetry And Length-Weight Relationship Of The Three Populations Of Sardinella Lemuru (Clupeiformes, Dorosomatidae) From Surigao Del Norte, Philippines

Fig. 1. The Philippine map showing the location of Caraga Region in Mindanao Island and the three sampling areas in the province of Surigao del Norte. Map credited to Engr. Medielyn M. Odtojan.

Fig. 3 in Fluctuating Asymmetry And Length-Weight Relationship Of The Three Populations Of Sardinella Lemuru (Clupeiformes, Dorosomatidae) From Surigao Del Norte, Philippines

Fig. 3. Principal components (PC) inferred deformation grid and histogram of individual (symmetry) in San Francisco, Surigao del Norte.

Fig. 13 in Diversity And Density Of Mollusca (Gastropoda And Bivalvia) Population In The Euphrates River At Al-Nasiriyah, Southern Iraq

Fig. 13. Dominance values of Mollusca species from July 2018 to June 2019 in the study stations at the Euphrates River.

Fig. 14 in Diversity And Density Of Mollusca (Gastropoda And Bivalvia) Population In The Euphrates River At Al-Nasiriyah, Southern Iraq

Fig. 14. Evenness values of Mollusca species from July 2018 to June 2019 in the study stations at the Euphrates River.

Fig. 1 in Diversity And Density Of Mollusca (Gastropoda And Bivalvia) Population In The Euphrates River At Al-Nasiriyah, Southern Iraq

Fig. 1. Shows the three study stations on the Euphrates River within Al-Nasiriyahcity. Yelow circle: station 1; blue circle: station 2; red cicle: station 3.

Fig. 11 in Diversity And Density Of Mollusca (Gastropoda And Bivalvia) Population In The Euphrates River At Al-Nasiriyah, Southern Iraq

Fig. 11. Shannon index values of Mollusca species from July 2018 to June 2019 in the study stations at the Euphrates River.