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Oenothera Section Calylophus population genetic study

Premise: Animal pollinators play an important role in pollen dispersal. Differences in foraging patterns, flight distances and grooming behaviors are assumed to have consequences for genetic diversity of plants but are rarely tested explicitly. Here, we assess the role of pollinator functional groups with different foraging behaviors (hawkmoth and bee) in generating patterns of genetic diversity over similar geographic ranges for two closely related taxa. Methods: This study focuses on two members of Oenothera section Calylophus that co-occur on gypsum outcrops throughout the Chihuahua Desert but differ in floral phenotype and primary pollinator: Oenothera gayleana (bee) and O. hartwegii subsp. filifolia (hawkmoth). We measured breeding system and floral traits in the greenhouse and conducted a population genetic study at the local (<13km; four populations) and landscape (60–440km; five populations) scales using 10–11 nuclear (pollen dispersal) and three plastid (seed dispersal) microsatellite markers. Key Results: Both taxa were self-incompatible and floral traits were consistent with expectations for different pollinators. We found no evidence of genetic structure at the local scale, but at the landscape scale, O. gayleana showed greater differentiation and significant isolation by distance than O. hartwegii subsp. filifolia. The plastid data were consistent with gravity dispersal of seeds and suggest that pollen dispersal is the principal driver of genetic structure in both species. Conclusions: We demonstrate that pollinator functional groups can impact genetic differentiation in different and predictable ways. Hawkmoths, with larger foraging distances, can maintain gene flow across greater spatial scales than bees.

Multilevel selection on social network traits differs between sexes in experimental populations of forked fungus beetles

Both individual and group behavior can influence individual fitness, but multilevel selection is rarely quantified on social behaviors. Social networks provide a unique opportunity to study multilevel selection on social behaviors, as they describe complex social traits and patterns of interaction at both the individual and group levels. In this study, we used contextual analysis to measure the consequences of both individual network position and group network structure on individual fitness in experimental populations of forked fungus beetles (Bolitotherus cornutus) with two different resource distributions. We found that males with high individual connectivity (strength) and centrality (betweenness) had higher mating success. However, group network structure did not influence their mating success. Conversely, we found that individual network position had no effect on female reproductive success but that females in populations with many social interactions experienced lower reproductive success. The strength of individual-level selection in males and group-level selection in females intensified when resources were clumped together, showing that habitat structure influences multilevel selection. Individual and emergent group social behavior both influence variation in components of individual fitness but impact male mating success and female reproductive success differently, setting up intersexual conflicts over patterns of social interactions at multiple levels.

Data from: Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation

Comparing divergence in quantitative traits and neutral molecular markers, such as QST–FST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into two geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesised to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (FST) with an index of phenotypic differentiation (PST). We used 7,562 putatively neutral single nucleotide polymorphisms (SNPs) across 15 populations and three clades of O. neglectus throughout New Zealand to infer FST. PST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades and shape groups. By systematically comparing PST with FST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.

Data and R computer code from: Summer elk calf survival in a partially migratory population

These data and computer code (written in R, https://www.r-project.org) were created to statistically evaluate a suite of intrinsic and extrinsic risk factors related to calf elk and their mothers' body condition and age. Specifically, known-fate data were collected from 94 elk calves monitored from 2013-2016 in a partially migratory elk (Cervus canadensis) population in Alberta, Canada. Along with adult female data on pregnancy status, age, and body condition, we created a time-to-event dataset that allowed us to analyze calf mortality risk in a time-to-event approach. We also estimated pooled survivorship and cause-specific mortality, as well as stratifying these metrics by migration tactic (resident vs. eastern migrant). Cox proportional hazards models were used to evaluate calf mortality risk in terms of forage biomass (kg/ha), bear predation risk (from an RSF), and other factors that varied between migration tactics. We tested for differences in a number of maternal reproductive parameters (e.g., pregnancy status) and for calf explanatory variables between migrant and resident elk segments. We also use cumulative incidence functions to estimate cause-specific mortality in this multiple carnivore system. Ultimately, we hope that this work helps wildlife managers anticipate how elk calf survival and partial migration dynamics are affected by grizzly bear predation, and our study builds on a long-term partial migration study at the Ya Ha Tinda Ranch in Alberta, Canada.

opencc-by-4.0Jul 2018View details →

Figure 1 in Effect of initial infestation on population fluctuation and spatial distribution of Panonychus citri (Acari: Tetranychidae) on Thomson navel orange in Ghaemshahr, Iran

Figure 1. Population fluctuation of Panonychus citri on Thomson navel orange in a multi-treatment experiment in in 2016. Control treatment = average number of 0.48 mite per leaf; Treatment 1 = average number of 1.12 mites per leaf, Treatment 2 = average number of 1.23 mites per leaf, Treatment 3 = average number of 6.36 mites per leaf, Treatment

opencc-by-4.0Jul 2018View details →

Figure 4 in Effect of initial infestation on population fluctuation and spatial distribution of Panonychus citri (Acari: Tetranychidae) on Thomson navel orange in Ghaemshahr, Iran

Figure 4. Population fluctuation of Panonychus citri on Thomson navel orange in a paired-treatment experiment in 2017. Infested treatment = average number of 0.79 mite per leaf, Control treatment = average number of 0.59 mite per leaf.

opencc-by-4.0Jul 2018View details →

Figure 2 in Effect of initial infestation on population fluctuation and spatial distribution of Panonychus citri (Acari: Tetranychidae) on Thomson navel orange in Ghaemshahr, Iran

Figure 2. Population fluctuation of Panonychus citri on Thomson navel orange in a multi-treatment experiment in in 2016. Control treatment = average number of 0.2 mite per leaf, Treatment 1 = average number of 0.3 mite per leaf, Treatment

Figure 5 in Effects of climatic parameters on Tetranychus urticae (Acari: Tetranychidae) populations based on remote sensing in the southeastern Caspian Sea

Figure 5. The relationship between UV Aerosol Index extracted from Sentinel-5 imagery and spider mite population (mean score of each window) from June 9, 2020 to September 17, 2020 (First window, May 30 to June 9 was not spider mite distribution data).

Figure 6 in Effects of climatic parameters on Tetranychus urticae (Acari: Tetranychidae) populations based on remote sensing in the southeastern Caspian Sea

Figure 6. The relationship between daily CHIRPS-precipitation and spider mite population (mean score of each window) from June 9, 2020 to September 17, 2020 (First window, May 30 to June 9 was not spider mite distribution data).

Figure 2 in Target-site insensitivity to some acaricides in a field population of Tetranychus urticae Koch (Acari: Tetranychidae) from Egypt

Figure 2. Multiple alignment of the amino acid sequences of T. urticae acetylcholinesterase (AChE) between Eg-Bernasht population and GenBank published populations. Tetranychus urticae AChE sequences were performed local as well as global alignments, using BLASTX search protein databases, using a translated nucleotide (NCBI). Three different specific primer sets (1, 2, and 3; Table 1) contained 422 amino acids of AChE gene. Dots: indicate amino acid similarity. Digital number: amino acid position on the AChE protein.

Figure 1 in Target-site insensitivity to some acaricides in a field population of Tetranychus urticae Koch (Acari: Tetranychidae) from Egypt

Figure 1. Products were imaged on a gel post electrophoresis. Tetranychus urticae acetylcholinesterase (AChE) gene fragment amplified expected sizes (639 bp, 571 bp, and 560 bp), using specific primers sets (1, 2, and 3, respectively). Tetranychus urticae voltage-gated sodium channel (VGSC) gene fragments were amplified products (226 bp, 225 bp, and 292 bp), using specific primers primer sets (4, 5, and 6, respectively). Tetranychus urticae glutamategated chloride channel (GluCl1, GluCl3) genes and chitin synthase 1 (CHS1) gene amplified products (263 bp, 251 bp, 541 bp), using primer sets (7, 8, and 9 respectively). EtBr was added to the gel before electrophoresis to a final concentration of 0.5 μg/ml, followed by separation at 100 V for 1 h. The gel was exposed to UV light and the picture was taken with a gel documentation system. Letter a: sample 1, letter b: sample 2, (-): no DNA templates. M:100 bp DNA ladder.

Figure 9 in Effects of climatic parameters on Tetranychus urticae (Acari: Tetranychidae) populations based on remote sensing in the southeastern Caspian Sea

Figure 9. The relationship between NDVI (10 m) provided form Sentinal-2 and density of spider mite during monitoring windows based on ANOVA for linear regression. The alphabetical letters indicate of the sequence windows from June 9, 2020 to September 17, 2020 (First window, May 30 to June 9 was not spider mite distribution data).

Figure 4 in Effects of climatic parameters on Tetranychus urticae (Acari: Tetranychidae) populations based on remote sensing in the southeastern Caspian Sea

Figure 4. Distribution maps of spider mite based on IDW model during monitoring windows, a–n are the sequence windows form June 9, 2020 to September 17, 2020 (First window, May 30 to June 9 was not spider mite population data).

Figure 8 in Effects of climatic parameters on Tetranychus urticae (Acari: Tetranychidae) populations based on remote sensing in the southeastern Caspian Sea

Figure 8. The relationship between MODIS-Evapotranspiration and spider mite population (mean score of each window) from June 9, 2020 to September 17, 2020. (First window, May 30 to June 9 was not spider mite distribution data).

Figure 3 in Effects of climatic parameters on Tetranychus urticae (Acari: Tetranychidae) populations based on remote sensing in the southeastern Caspian Sea

Figure 3. Spider mite distribution throughout Golestan province; 6 (min.) × 6 (min.) grid cells in the DMS coordinate system (yellow points indicate the monitoring fields).

opencc-zeroDec 2021View details →

Pest defenses under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations

Whilst droughts, intensified by climate change, have been affecting forests worldwide, pest epidemics are a major source of uncertainty for assessing drought impacts on forest trees. Thus far, little information has documented the adaptability and evolvability of traits related to drought and pests simultaneously. We conducted common-garden experiments to investigate how several phenotypic traits (i.e., height growth, drought avoidance based on water-use efficiency inferred from δ13C, and pest resistance based on defense traits) interact in five mature lodgepole pine populations established in four progeny trials in western Canada. The relevance of interpopulation variation in climate sensitivity highlighted that seed-source warm populations had greater adaptive capability than cold populations. In test sites, warming generated taller trees with higher δ13C and increased the evolutionary potential of height growth and δ13C across populations. We found, however, no pronounced gradient in defenses and their evolutionary potential along populations or test sites. Response to selection was weak in defenses across test sites, but high for height growth, particularly at warm test sites. Response to selection of δ13C varied depending on its selective strength relative to height growth. We conclude that warming could promote the adaptability and evolvability of growth response and drought avoidance with limited evolutionary influence from pest (biotic) pressures.

opencc-by-4.0Oct 2022View details →

Construction of a SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

The VCF file contains the information of 1662 SNP sites of 820 cauliflower inbred lines that were filtered according to a series of stringent conditions.

Assessing the value of monitoring to biological inference and expected management performance for a European goose population

1. Informed conservation and management of wildlife require sufficient monitoring to understand population dynamics and to direct conservation actions. Because resources available for monitoring are limited, conservation practitioners must strive to make monitoring as cost-effective as possible. 2. Our focus was on assessing the value of monitoring to the adaptive harvest management (AHM) program for pink-footed geese (Anser brachyrhynchus). We conducted a retrospective analysis to assess the costs and benefits of a capture-mark-resight (CMR) program, a productivity survey, and biannual population censuses. Using all available data, we fit an integrated population model (IPM) and assumed that inference derived from it represented the benchmark against which reduced monitoring was to be judged. We then fit IPMs to reduced sets of monitoring data and compared their estimates of demographic parameters and expected management performance against the benchmark IPM. 3. Costs and the precision and accuracy of key demographic parameters decreased with the elimination of monitoring data. Eliminating the CMR program, while maintaining other monitoring instruments, resulted in the greatest cost savings, usually with small effects on inferential reliability. Productivity surveys were also expensive and some reduction in survey effort may be warranted. The biannual censuses were inexpensive and generally increased inferential reliability. 4. The expected performance of AHM strategies was surprisingly robust to a loss of monitoring data. We attribute this result to explicit consideration of parametric uncertainty in harvest-strategy optimization and the fact that a broad range of population sizes is acceptable to stakeholders. 5. Synthesis and applications: Our study suggests that existing or potential monitoring instruments for wildlife populations should be scrutinized as to their cost-effectiveness for improving biological inference and management performance. Using Svalbard pink-footed geese as a case study, we show that the loss of some existing monitoring instruments may not be as adverse as commonly assumed if data are jointly analyzed in an integrated population model. Finally, regardless of the monitoring data available, we suggest that conservation strategies that explicitly account for uncertainty in demography are more likely to be successful than those that do not.

Data from: Protection status, human disturbance, snow cover and trapping drive density of a declining wolverine population in the Canadian Rocky Mountains

Protected areas are important in species conservation, but high rates of human-caused mortality outside their borders and increasing popularity for recreation can negatively affect wildlife populations. We quantified wolverine (Gulo gulo) population trends from 2011 to 2020 in >14 000 km2 protected and non-protected habitat in southwestern Canada. We conducted wolverine and multi-species surveys using non-invasive DNA and remote camera-based methods. We developed Bayesian integrated models combining spatial capture-recapture data of marked and unmarked individuals with occupancy data. Wolverine density and occupancy declined by 39 percent, with an annual population growth rate of 0.925. Density within protected areas was 3 times higher than outside and declined between 2011 (3.6 wolverines/1000 km2) and 2020 (2.1 wolverines/1000 km2). Wolverine density and detection probability increased with snow cover and decreased near development. Detection probability also decreased with human recreational activity. The annual harvest rate of 13% was above the maximum sustainable rate. We conclude that humans negatively affected the population through direct mortality, sub-lethal effects and habitat impacts. Our study exemplifies the need to monitor population trends for species at risk – within and between protected areas - as steep declines can occur unnoticed if key conservation concerns are not identified and addressed.