Additional file 1 of The multivariate analysis of variance as a powerful approach for circular data

Additional file 1. R-code and example data to perform the statistical tests described in the manuscript

Data from: Methods in field chronobiology

Chronobiological research has seen a continuous development of novel approaches and techniques to measure rhythmicity at different levels of biological organization from locomotor activity (e.g. migratory restlessness) to physiology (e.g. temperature and hormone rhythms, and relatively recently also in genes, proteins and metabolites). However, the methodological advancements in this field have been mostly and sometimes exclusively used only in indoor laboratory settings. In parallel, there has been an unprecedented and rapid improvement in our ability to track animals and their behaviour in the wild. However, while the spatial analysis of tracking data is widespread, its temporal aspect is largely unexplored. Here, we review the tools that are available or have potential to record rhythms in the wild animals with emphasis on currently overlooked approaches and monitoring systems. We then demonstrate, in three question-driven case studies, how the integration of traditional and newer approaches can help answer novel chronobiological questions in free-living animals. Finally, we highlight unresolved issues in field chronobiology that may benefit from technological development in the future. As most of the studies in the field are descriptive, the future challenge lies in applying the diverse technologies to experimental set-ups in the wild. This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.,Annotated GPS tracking dataAnnotated GPS-tracking data used to create Figure 2 (Example of daily foraging rhythms in three Montagu’s Harriers). One file is included per bird. The zip files includes a word file describing the different columns.

Data from: Contagious fear: escape behaviour increases with flock size in European gregarious birds

Flight initiation distance (FID), the distance at which individuals take flight when approached by a potential (human) predator, is a tool for understanding predator-prey interactions. Among the factors affecting FID, tests of effects of group size (i.e. number of potential prey) on FID have yielded contrasting results. Group size or flock size could either affect FID negatively (i.e. the dilution effect caused by the presence of many individuals) or positively (i.e. increased vigilance due to more eyes scanning for predators). These effects may be associated with gregarious species, because such species should be better adapted to exploiting information from other individuals in the group than non-gregarious species. Sociality may explain why earlier findings on group size vs. FID have yielded different conclusions. Here, we analyzed how flock size affected bird FID in eight European countries. A phylogenetic generalized least square regression model was used to investigate changes in escape behavior of bird species in relation to number of individuals in the flock, starting distance, diet, latitude and type of habitat. Flock size of different bird species influenced how species responded to perceived threats. We found that gregarious birds reacted to a potential predator earlier (longer flight initiation distance) when aggregated in large flocks. These results support a higher vigilance arising from many eyes scanning in birds, suggesting that sociality may be a key factor in the evolution of anti-predator behavior both in urban and rural areas. Finally, future studies comparing FID must pay explicit attention to the number of individuals in flocks of gregarious species.,dataset.fid.gregarious.2019Dataset associated to the article "Contagious fear: Escape behaviour increases with flock size in European gregarious birds" by Morelli et al. 2019. Metadata: Variable Details Species Species latin name FID_mean Flight initiation distance measured in meters (mean value) n No. observations of FID initiation Starting distance species Scientific name diet.specific Type of diet gregariousness gregarious bdm.quant body mass quartile latitude Latitude in decimel degrees habitat Type of habitat: Rural or urban flock Flock size (individuals) bodymass body mass (g)

Evidence for reduced immune gene diversity and activity during the evolution of termites

This dataset contains data from a termite immunity related study described in the paper: “He Shulin, Sieksmeyer Thorben, Che Yanli, Mora M. Alejandra Esparza, Stiblik Petr, Banasiak Ronald, Harrison Mark C., Šobotník Jan, Wang Zongqing, Johnston Paul R. and McMahon Dino P. 2021Evidence for reduced immune gene diversity and activity during the evolution of termitesProc. R. Soc. B.288:20203168.http://doi.org/10.1098/rspb.2020.3168”. The study investigates the evolution of termite molecular immune system: evolution of immune gene family along a constructed phylogeny, different individual immune response between three termite castes, a subsocial cockroach and a non-social cockroach, the caste specific expression of immune genes, different social immune response between a social termite species and a non-social cockroach species. In the first experiment, we de novo sequenced 18 cockroach and termite species, spanning the full spectrum of solitary and social lifestyles, including two solitary cockroach species, two species of subsocial Cryptocercus wood-feeding cockroaches and 14 termite species. We exploited a transcriptomic approach to compare the immune gene repertoire of these sequenced species. In the second experiment, we compared individual immune responses in a solitary cockroach, B. orientalis, a subsocial wood-feeding roach, Cryptocercus meridianus, and each caste of a social termite, Neotermes castaneus, following direct injection with heat-killed microbes. In the third experiment, we explored total gene expression differences between castes without immune challenge. In the fourth experiment, we studied gene expression changes in each caste of N. castaneus following colony exposure to immune-challenged nestmates, and compared these with gene expression changes in the solitary cockroach, B. orientalis, following group exposure to immune-challenged conspecifics. Main results of the experiments are that (1) immune gene families show contractions and expansions during temite evolution; (2) compared with cockroaches, termites showed weak individual immune response; (3) termites have caste-specific constitutive immunity; (4) Compared with cockroach, termite showed a stronger gene expression changes in response to a social immune challenge

Data from: Scrutinizing assortative mating in birds

It is often claimed that pair bonds preferentially form between individuals that resemble one another. Such assortative mating appears to be widespread throughout the animal kingdom. Yet it is unclear whether the apparent ubiquity of assortative mating arises primarily from mate choice (‘like attracts like’) which can be constrained by same-sex competition for mates, from spatial or temporal separation, or from observer, reporting, publication or search bias. Here, based on a conventional literature search, we find compelling meta-analytical evidence for size-assortative mating in birds (r = 0.178, 95% CI: 0.142 – 0.215, 83 species, 35,591 pairs). However, our analyses reveal that this effect vanishes gradually with increased control of confounding factors. Specifically, the effect size decreased by 42% when we used unpublished data from nine long-term field studies, i.e. data free of reporting and publication bias (r = 0.103, 95% CI: 0.074 – 0.132, eight species, 16,611 pairs). Moreover, in those data assortative mating effectively disappeared when both partners were measured by independent observers or separately in space and time (mean r = 0.018, 95% CI: -0.016 – 0.057). Likewise, we also found no evidence for assortative mating in a direct experimental test for mutual mate choice in captive populations of zebra finches (r = -0.020, 95% CI: -0.148 – 0.107, 1,414 pairs). These results highlight the importance of unpublished data in generating unbiased meta-analytical conclusions, and suggest that the apparent ubiquity of assortative mating reported in the literature is overestimated and may not be driven by mate choice or mating competition for preferred mates.,S1_Data.xlsxUnpublished data (nine long-term field studies): All the pairs that have been identified across the nine studies where both pair members have at least one morphological record, including repeated records from different years. This dataset also includes latitude and longitude of the nest site (Lambert azimuthal equal-area projection, units = meters) and year and, if available, the putative date of the first egg.Supplementary_file_1_unpublished_data1.xlsxS2_Data.xlsxUnpublished data (nine long-term field studies): All available records of morphological traits which covered more than 95% of individuals included in S1_Data.This dataset also includes the location where the individual was caught, the date of catching, and the observer who measured the individualSupplementary_file_2_unpublished_data2.xlsxS3_Data.xlsxUnpublished data (nine long-term field studies): Data where we combined the information from data S1_Data and S2_DataSupplementary_file_3_unpublished-data3.xlsxS4_Data_xlsxPublished data (Fig 1A): Excel spreadsheet containing two separate sheets with data from literature: 1) data extracted from the publications and 2) the original references.Literature_data.xlsxS5_Data_xlsxData for Fig 1B: Strength of assortative mating for size as a function of data source.Pearons_r_different_data_sources_integrated_mixed_model.xlsxS6_Data_xlsxModels for the unpublished data (Fig 1C): Excel spreadsheet contains 6 separate sheets; each sheet corresponds to a model to estimate the strength of assortative mating.Models_of_unpublished_data.xlsxS7_Data,xlsxData for Fig 2: Strength of assortative mating for body size in relation to sample size.Funnel_plot_asymmetry_test.xlsxS8_Data.xlsxExperimental data on zebra finches. The zebra finches data include five experiments.Experimental data_zebra_finch.xlsxPRISMA_literature summaryThe process of literature investigation.PRISMA_summary of literature.docx

Additional file 2: of Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog

Figure S2. Genetic variability indexes computed in SVS using the 126k SNP dataset. a Mean values of observed heterozygosity (Ho) within groups. Czechoslovakian Wolfdogs (in dark gray) show higher levels of heterozygosity than parental populations (Carpathian wolves in black and German Shepherds in light grey), as expected from the recent crossings that originated the breed, but lower than most breeds. Bars indicate standard deviations. b Plots of the mean inbreeding coefficient F per breed. Czechoslovakian Wolfdogs show a mean F value intermediate among the other breeds but lower than both parental populations. c: from left to right: individual F values for Carpathian wolf (black histograms), German Shepherd (light grey histograms) and Czechoslovakian Wolfdog (dark gray histograms) groups. Bars indicate standard deviations. (PDF 94 kb

Additional file 8: of Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog

Figure S7a. BGC alpha parameter outlier SNPs. Values lower than 0 indicate excess of wolf alleles, values higher than 0 indicate excess of dog alleles. BGC significant outliers are indicated by blue crosses (top or bottom 1% of the empirical distribution of values) and by red dots (95% credibility intervals of 10,000 iterations not including 0). Figure S7b. BayeScan outlier SNPs detected comparing differences in allele frequency between Czechoslovakian Wolfdogs and German Shepherds (right) and between Czechoslovakian Wolfdogs and Carpathian wolves (left). The vertical axis indicates mean FST values between populations, and the horizontal axis indicates the logarithm of posterior odds (log(PO)). The vertical line indicates the log(PO) value corresponding to the false discovery rate threshold of 0.05. Loci on the right of this line are putatively under selection. (PDF 312 kb

Additional file 4: of Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog

Figure S4. Comparison between the individual frequency of ROHs (FROH), calculated in SVS as the proportion of ROHs on the genome length spanned by the analysed SNPs (on the horizontal axis), and the individual Wright’s inbreeding coefficient (COI), estimated from the pedigrees with the software U-WGI (on the vertical axis). The two inbreeding indexes are significantly (p < 0.01) correlated. (PDF 71 kb

Additional file 5: of Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog

Figure S5. Linkage disequilibrium (LD) decay plot. The vertical axis indicates the mean Estimated R-squared (r2), and the horizontal axis indicates the distance in kb at which LD decays. (PDF 220 kb

Additional file 6: of Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog

Figure S6. Graphical representation, for each chromosome of each analysed Czechoslovakian Wolfdog, of the ancestry components identified by PCAdmix based on the analysis of 10-SNP haplotype blocks. Each horizontal bar represents the two homologous chromosomes of an individual showing in black the genomic regions assigned as wolf-like and in light grey those assigned as dog-like. (PDF 10810 kb