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Additional file 5. Wilcoxon Rank Sum Test results on differential abundance of bacterial genera between Eurasian magpies and great spotted cuckoos from mono- (M) or hetero-specific (H) nests. Group column refers to the group with higher abundance of the specific strain., Ministerio de Ciencia e Innovación European Regional Development Fund Consejo Superior de Investigaciones Cientificas (CSIC), Peer reviewed

Additional file 6. Subset of the ASV table with six taxonomic levels including ASVs classified as core-microbiome in Eurasian magpies or great spotted cuckoos. Samples are identified regarding species and whether they share or not share the nest with hetero-specifics., Ministerio de Ciencia e Innovación European Regional Development Fund Consejo Superior de Investigaciones Cientificas (CSIC), Peer reviewed

Fundación Biodiversidad from the Spanish Ministry for the Ecological Transition and the Demographic Challenge (project LIFE19/NAT/ES/000906)., Peer reviewed

The Natural Sciences and Engineering Research Council (NSERC) of Canada Canada Foundation for Innovation (CFI) G. Unger Vetlesen and Ambrose Monell Foundations National Science Foundation Gordon and Betty Moore Foundation Investigator Award, Peer reviewed

Peer reviewed

The dataset contains all the input files used to perform the analyses described in the paper, Peer reviewed

The success of amphibian conservation efforts is highly dependent on the preservation of amphibian breeding habitats. Doñana National Park contains an abundance of ponds with heterogeneous characteristics, which has historically favoured its amphibian community. However, most of the park’s ponds are groundwater dependent, and aquifer overexploitation outside the park is leading to shorter hydroperiods and even desiccation in the pond network. This problem has been exacerbated by the scarcity of rain over the last decade. In 2021–2022, we surveyed the occurrence of the park’s 11 amphibian species, with a view to comparing our findings with those from the last previous survey in 2003–2004. We mapped the species occurrence within the park for the two survey periods. While all 11 amphibian species could still be found in Doñana, their occurrence had decreased across the board. In 2003–2004, 6 species were present across more than 50% of the sampling area. In contrast, 18 years later, such was the case for only two species (Pelophylax perezi and Hyla meridionalis). Declines were greatest for Epidalea calamita, followed by Pelobates cultripes, Triturus pygmaeus, and Lissotriton boscai. The mean number of species per sampling unit (i.e., grid cell) dropped from 4.3 to 3.1. To preserve Doñana’s amphibian community, it is important to restore the park’s pond network, which implies reducing regional groundwater overexploitation., Peer reviewed

Description of Experiment and Data Collection This experiment was conducted at the Danum Valley Field Centre (N04.96° E117.80°; 180 MASL), Sabah, Malaysia. The field centre is part of the Danum Valley Conservation Area (DVCA), a 43800-ha area of primary lowland forest dominated by the Family Dipterocarpaceae (dipterocarps). The experiment was planted in November 2004 throughout the primary forest south and west from the field centre. Twenty plots were placed across a large size range (12 – 400 m2) of natural canopy openings (gaps) and paired with identical plots under closed canopy (understorey) Understorey sites were placed 30 meters from each tree-fall gap at a random compass bearing. The combined gap and understorey plots represent a block. Blocks were placed across the range of topography found in Danum Valley whereby 6 blocks were in lowland riparian areas, 7 blocks were in lowland areas away from rivers and 7 blocks were on upslope sites (Fig. S1 in the Supplementary Information). The mean elevation across all plots was 249 m (range = 203 – 319 m) and the mean slope was 20 degrees (range = 3 – 56 degrees). Within each gap and understorey plot, two identical subplots were planted with seedlings of 25 tree species at 0.75 × 0.75 m spacing for a total of four subplots per gap-understorey pair and a total of 80 subplots (20 pairs × 2 gap/understorey plots × 2 subplots = 80 subplots). Due to the infrequent seed production of tree species in lowland Borneo forests, species were selected mainly based on availability in local nurseries (see Table S3 in Supplementary Information for species information). Twenty-four species were dipterocarps spanning five genera (Dipterocarpus, Dryobalanops, Hopea, Parashorea and Shorea) and one species of Bombaceae (Durian graveolens). Within each subplot, species were randomly assigned a planting point, therefore, all 80 subplots had a different planting pattern. Six months after planting—to allow for mortality due to planting stress (which was replanted after one and three months—seedlings were measured for height and diameter at base (10 cm from soil surface). From 2004 to 2007 seedlings were measured every 6 months after which they were measured approximately yearly from 2007 to 2017. One census was not included in this analysis because as it was measured only 3 months after the previous census, which led to a total of 16 censuses. These measurements of growth were used to calculate relative growth rate as the difference in log-diameter between two measurements divided by the number of days between measurements standardized to year by dividing days by 365.25. Description of each column in DataGrowthSurvivalClean.txt Block - Gap/understorey pair (Categorical variable from 1 to 20) pid - Plot ID (Categorical variable of 40 plots) Survey.date - Date of measurement (DD/MM/YYYY) Day - Julian day Year - Year of census Census - Census number Canopy - Gap or understorey designation (Categorical variable U/G) Plot - Plot number (Categorical variable from 1 to 40) Subplot - Subplot within plot (Categorical variable A/B) Subplot.no - Subplot number (Categorical variable from 1 to 80) Genus - Genus Species - Specific epithet Sp - Unique ID of first 3 letters of genus and first 3 letters of specific epithet Plant.id - ID for each individual (Categorical variable from 1 to 2000) Diam1 - Diameter at base measurement Diam2 - Diameter at base measurement DBH.1 - Diameter at breast height of taller than 1.3 m DBH.2 - Diameter at breast height of taller than 1.3 m Height.apex - Height to apical bud diam - Average of two diameter measurements dbh - Average of two DBH measurements light - Percent light in the plot measured at the start of the experiment deficit - Minimum 30-day average of rainfall deficit since last census zero - Number of days with no rain since last census dry - Number of days of the longest dry period since last census excess - Maximum 30-day average of rainfall excess since last census sun - Average sun hour per day since last census rain - Designation of rainfall conditions since last census (Wet > -50 mm deficit, Dry <-50 and >-100 mm deficit, Drought <-100 mm deficit) treat - Designation if plastic sheeting was applied to plot for the period (Everwet no plastic, Drought plastic rainfall exclusion) surv - Survival at census (1 = alive, 0 = dead) rgr - Relative growth rate for diameter at base elev - Plot elevation slp - Slope of plot topo - Designation of plot location (Categorical variable of Lowland, Riparian and Ridge) Description of RCode GrowthSurvivalGlobalFinal.R - Code for analysis of global growth and survival Figures 2 and 3 PlotsSpeciesResponses.R - Code to generate Figure 4 and 5 from Rstanarm output FitnessDifferences.R - Code to generate Figure 6 from Rstanarm output, Comunidad de Madrid Atracción de Talento Investigador2018-T1/AMB-11095 Agencia Estatal de Investigación Ramon y CajalRYC2021-032049-I, Peer reviewed

El dataset se puede consultar y descargar en el siguiente enlace https://doi.org/10.5061/dryad.bk3j9kdnc, Habitat association has been proposed to affect evolutionary dynamics through its control on dispersal propensity, which is considered a key trait for lineage survival in habitats of low durational stability. The Habitat Constraint hypothesis predicts different micro- and macroevolutionary patterns for stable vs. dynamic habitat specialists, but the empirical evidence remains controversial and in insects mostly derives from winged lineages. We here use genome-wide SNP data to assess the effect of habitat association on the population dynamics of two closely related flightless lineages of the genus Eutagenia (Coleoptera: Tenebrionidae), which are co-distributed across the Cyclades islands in the Eastern Mediterranean but are associated with habitat types of different presumed stability: the psammophilous lineage is associated with dynamic sandy coastal habitats, while the geophilous lineage is associated with comparatively stable compact-soil habitats. Our comparative population genomic and demographic analyses support higher inter-island gene flow in the psammophilous lineage, presumably due to the physical properties of dynamic sand-dune habitats that promote passive dispersal. We also find consistent bottlenecks in the psammophilous demes, suggesting that lineage evolution in the dynamic habitat is punctuated by local extinction and recolonisation events. The inferred demographic processes are surprisingly uniform among psammophilous demes, but vary considerably among geophilous demes depending on historical island connectivity, indicating more stringent constraints on the dynamic-habitat lineage. This study extends the Habitat Constraint hypothesis by demonstrating that selection on dispersal traits is not the only mechanism that can drive consistent differences in evolutionary dynamics between stable vs. dynamic habitat specialists., Research and Innovation Foundation : EXCELLENCE/0421/0419, Peer reviewed

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