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File S11. The sequences of Stellaris probes for Rsp
No full textThe following Stellaris probes are tagged with Quasar 570 and used to detect Rsp sequences
File S12. The fasta alignment of genomic IGS sequences from D. melanogaster and outgroup species
No full textWe extracted all IGS elements from the genome using BLAST v2.7.1 with parameters “- task blastn -num_threads 24 -qcov_hsp_perc 90” and custom scripts. We then aligned and manually inspected IGS sequences using Geneious v8.1.6
File S14. The newick consensus tree of IGS sequences inferred using RAxML
No full textWe constructed maximum likelihood phylogenetic trees for IGS using RAxML v.8.2.11 with parameters “-m GTRGAMMA -T24 -d -p 12345 -# autoMRE -k -x 12345 -f a”
Data from: Numerical cognition in honeybees enables addition and subtraction
No full textMany animals understand numbers at a basic level for use in essential tasks such as foraging, shoaling, and resource management. However, complex arithmetic operations, such as addition and subtraction, using symbols and/or labeling have only been demonstrated in a limited number of nonhuman vertebrates. We show that honeybees, with a miniature brain, can learn to use blue and yellow as symbolic representations for addition or subtraction. In a free-flying environment, individual bees used this information to solve unfamiliar problems involving adding or subtracting one element from a group of elements. This display of numerosity requires bees to acquire long-term rules and use short-term working memory. Given that honeybees and humans are separated by over 400 million years of evolution, our findings suggest that advanced numerical cognition may be more accessible to nonhuman animals than previously suspected
Simulation script
No full textThe R script used to perform the simulations presented in the main text of the articl
Simmonds_etal_JAE_thresholds
No full textFile provides the data used to examine thresholds in the richness-natural land cover relationship, among landscape with different attributes
Data from: Visual adaptation and microhabitat choice in Lake Victoria cichlid fish
No full textWhen different genotypes choose different habitats to better match their phenotypes, adaptive differentiation within a population may be promoted. Mating within those habitats may subsequently contribute to reproductive isolation. In cichlid fish, visual adaptation to alternative visual environments is hypothesised to contribute to speciation. Here, we investigated whether variation in visual sensitivity causes different visual habitat preferences, using two closely related cichlid species that occur at different but overlapping water depths in Lake Victoria and that differ in visual perception (Pundamilia sp.). In addition to species differences, we explored potential effects of visual plasticity, by rearing fish in two different light conditions: broad-spectrum (mimicking shallow water) or red-shifted (mimicking deeper waters). Contrary to expectations, fish did not prefer the light environment that mimicked their typical natural habitat. Instead, we found an overall preference for the broad-spectrum environment. We also found a transient influence of the rearing condition, indicating that assessment of microhabitat preference requires repeated testing to control for familiarity effects. Together, our results show that cichlid fish exert visual habitat preference, but do not support straightforward visual habitat matching
Metadata of studies examining reproductive traits before and after whole genome duplication
No full textThis dataset contains metadata collected from publications that were used for the analyses in our study. It includes information about the study species and measurements of traits before and after whole genome duplication