Additional file 7: Table S2. Table of relative abundances of Synechococcus MAGs in Ircinia, inferred via CoverM.

Additional file 8: Table S3. Table of genes and domains that are significantly enriched or depleted in Ircinia, and which are plotted in Fig. 2.

Predicting forest recovery at landscape scales will aid forest restoration efforts. The first step in successful forest recovery is tree recruitment. Forecasts of tree recruit abundance, derived from the landscape-scale distribution of seed sources (i.e. adult trees), could assist efforts to identify sites with high potential for natural regeneration. However, previous work has revealed wide variation in the effect of seed sources on seedling abundance, from positive to no effect. We quantified the relationship between...

Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamental roles in host nutrition and immunity. We find significant differences in the gut microbiome composition of a facultative coral-feeding butterflyfish (Chaetodon capistratus) across Caribbean reefs that differ markedly in live coral cover (∼0–30%). Fish gut microbiomes...

Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological datasets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in datasets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become...

Lightning is an important agent of mortality for large tropical trees with implications for tree demography and forest carbon budgets. We evaluated interspecific differences in susceptibility to lightning damage using a unique dataset of systematically located lightning strikes on Barro Colorado Island, Panama. We measured differences in mortality among trees damaged by lightning and related those to damage frequency and tree functional traits. Eighteen of 30 focal species had lightning mortality rates that deviated from...

Understanding the effect of body size on flight costs is critical for development of models of aerodynamics and animal energetics. Prior scaling studies that have shown that flight costs scale hypometrically have focused primarily on larger (> 100 mg) insects and birds, but most flying species are smaller. We studied the flight physiology of thirteen stingless bee species over a large range of body sizes (1-115 mg). Metabolic rate during hovering scaled hypermetrically (scaling slope...

Examining how environmental factors influence phenotypic distribution might provide valuable information about local adaptation, divergence, and speciation. The red-yellow Müllerian mimicry ring of Heliconius butterflies displays a wide range of color patterns across the Neotropics and is involved in several hybrid zones, making it an excellent system to study color phenotypic distribution. Using a multiscale distribution strategy, we studied whether different phenotypes of the distantly related species H. erato and H. melpomene, belonging to the...

The transition from the Medieval Climate Anomaly (MCA, 950-1250 CE) to the Little Ice Age (LIA, 1350 to 1800 CE) is the largest pre-industrial climate shift within the last two millennia, offering an opportunity to study how vegetation responds to rapid climate change. We analyzed a sedimentary record from the Colombian Andes to reconstruct regional vegetation dynamics during this time interval, identify the modern environmental distribution of taxa present in the fossil record, and provide...

Pre-dispersal seed mortality caused by premature fruit drop is a potentially important source of plant mortality, but one which has rarely been studied in the context of tropical forest plants. Of particular interest is premature fruit drop triggered by enemies, which – if density-dependent – could contribute to species co-existence in tropical forest plant communities. We used a long-term (31 year) dataset on seed and fruit fall obtained through weekly collections from a network of...

Organisms of all species must balance their allocation to growth, survival and recruitment. Among tree species, evolution has resulted in different life-history strategies for partitioning resources to these key demographic processes. Life-history strategies in tropical forests have often been shown to align along a trade-off between fast growth and high survival, i.e. the well-known fast-slow continuum. In addition, an orthogonal trade-off has been proposed between tall stature – resulting from fast growth and high survival...

Integrating and weighting sensory perception across modalities is crucial to how animals adapt to their environment. Divergence in brain structure is often in sensory processing regions, suggesting that investment reflects ecological needs. Here, we use two parapatric closely related species, Heliconius erato cyrbia and Heliconius himera, to test the hypothesis that divergence in sensory brain regions affects foraging decisions. These butterflies are isolated across an ecological gradient, which is linked to differences in brain morphology,...

Early predator detection is a key component of the predator-prey arms race and has driven the evolution of multiple animal hearing systems. Katydids (Insecta) have sophisticated ears, each consisting of paired tympana on each foreleg that receive sound both externally, through the air, and internally via a narrowing ear canal running through the leg from an acoustic spiracle on the thorax. These ears are pressure-time difference receivers capable of sensitive and accurate directional hearing across...

Additional file 8: Table S3. Table of genes and domains that are significantly enriched or depleted in Ircinia, and which are plotted in Fig. 2.

Additional file 10: Data File S1. Fasta-formatted CSGs found in bacterial symbionts of Ircinia.

To forage efficiently, animals should selectively attend to and remember the cues of food that best predict future meals. One hypothesis is that animals with different foraging strategies should vary in their reliance on spatial versus feature cues. Specifically, animals that store food in dispersed caches or that feed on spatially stable food, like fruit or flowers, should be relatively biased to learning a meal’s location, whereas predators that hunt mobile prey should instead be...

The specificity of pollinator host choice influences opportunities for reproductive isolation in their host plants. Similarly, host plants can influence opportunities for reproductive isolation in their pollinators. For example, in the fig and fig wasp mutualism, offspring of fig pollinator wasps mate inside the inflorescence that the mothers pollinate. Although often host specific, multiple fig pollinator species are sometimes associated with the same fig species, potentially enabling hybridization between wasp species. Here we study the...

Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth’s diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns...

The sea urchins Echinothrix calamaris and E. diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discreet clades. One clade was endemic to...

Environmental fluctuations are becoming increasingly volatile in many ecosystems, highlighting the need to better understand how stochastic and deterministic processes shape patterns of commonness and rarity, particularly in high-diversity systems like coral reefs. We analyzed reef fish time-series across the Great Barrier Reef to show that approximately 75% of the variance in relative species abundance is attributable to deterministic, intrinsic species differences. Nevertheless, the relative importance of stochastic factors is markedly higher on reefs that...

Woody plant species were surveyed at 72 locations near the Panama Canal, spanning geological formations and a rainfall gradient. Soil chemistry, and dry season intensity at all the sites. Response of tree species to environmental gradients was estimated. The soil and climate data are provided in a single table here. Tree distributions are published at Condit et al. (2013a), including a data archive in Condit et al. (2013b). Note that the PNAS article incorrectly cites...

Females of many species choose mates using multiple sensory modalities. Multimodal noise may arise, however, in dense aggregations of animals communicating via multiple sensory modalities. Some evidence suggests multimodal signals may not always improve receiver decision-making performance. When sensory systems process input from multimodal signal sources, multimodal noise may arise and potentially complicate decision-making due to the demands on cognitive integration tasks. We tested female túngara frog, Physalaemus (=Engystomops) pustulosus, responses to male mating signals...

Additional file 10: Data File S1. Fasta-formatted CSGs found in bacterial symbionts of Ircinia.

Additional file 6: Table S1. Taxonomy, statistics, source metadata, and CSG occurrence in MAGs that passed QC and dereplication steps and were used in the final analyses. The archaeal MAGs and the Trichodesmium MAG that did not meet the completeness threshold are included.

Additional file 7: Table S2. Table of relative abundances of Synechococcus MAGs in Ircinia, inferred via CoverM.