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1. Woody encroachment into grassy biomes is a global phenomenon, often resulting in a nearly complete turnover of species, with savanna specialists being replaced by forest-adapted species. Understanding the mechanisms involved in this change is important for devising strategies for managing savannas. 2. We examined how isolated trees favor woody encroachment and species turnover by overcoming dispersal limitation and environmental filtering. In a savanna released from fire in southeastern Brazil (Cerrado) we sampled woody plants establishing under 40 tree canopies and in paired treeless plots. These trees comprised eight species selected for habitat preference (savanna or forest) and dispersal syndrome (bird-dispersed or not). We recorded dimensions of each tree, dispersal syndrome and habitat preference of recruits, and quantified the physical environment within each plot, aiming at a mechanistic understanding of woody encroachment. 3. We found clear evidence that isolated trees cause nucleation and drive changes in functional composition of savanna. Effectiveness as nucleator differed among species, but was unrelated to their functional guilds (habitat preference or dispersal syndrome). Density of saplings in nuclei was partially explained by soil moisture (+), daily temperature amplitude (-), and sum of bases (-). 4. Our results indicate that isolated trees act first as perches, strongly favoring bird-dispersed species. They then act as nurse trees, considerably changing the environment in favor of forest-adapted recruits. In the long term, as the nuclei expand and merge, savanna specialists tend to disappear and the savanna turns into a low-diversity forest. 5. Synthesis and applications: Fire suppression has allowed the nucleation process and consequently the woody encroachment and fast replacement of savanna specialists by forest species in the Cerrado. By elucidating the mechanisms behind woody encroachment, we recommend using prescribed fires to burn forest seedlings and to reduce tree canopy size wherever the management goal is to maintain the typical savanna structure and composition. Please see Methods in the article published in the Journal of Applied Ecology.

Facilitation and competition among plants sharing pollinators have contrasting consequences for each species' fitness. However, it is unclear whether pollinator-mediated indirect interactions between plants affect plant fitness in a multispecies context. Here, we investigated how pollinator sharing affects pollen limitation (contribution of pollination to fitness) in a tropical hummingbird-pollinated community marked by facilitation. We employed indices describing how much a plant species is important to shared pollinators (acting degree) and have its shared pollinators influenced by other plants (target degree) within the plant-hummingbird network. Since facilitation often increases pollination quantity but not necessarily quality, we expected both indices to be associated with reductions in pollen limitation estimates that depend on pollination quantity (fruit set and seed number) rather than estimates more strictly related to quality (seed weight and germination). Instead, we found that both indices were associated with reductions in pollen limitation only for seed weight and germination. Thus, facilitation acted on qualitative estimates of pollen limitation. Our results suggest that facilitation may enhance plant fitness even if quantitative components of plant fecundity are already saturated. Overall, we showed that pollinator-mediated indirect effects in a multispecies context are important drivers of plant fitness with consequences for coexistence in diverse communities.

Scenario for Jacaranda copaiaAll parameters (ecological, reproductive and genetic) of Jacaranda copaia to run Eco-gene program.jacaranda controle.txtJacaranda_genetic_inputThis file consists of the genetic input for running the simulations on Ecogene program. The file contains the number of individuals, coordinates (2 columns), dbh (diameter at breast height) and genotypes of 5 microsatellite markersJacaranda_Ecogeneseeds.txtMortality data of Jacaranda copaiaThis file consists of the mortality data of Jacaranda copaia, the file contains: first line is the header, second line is the number of dbh (diameter at breast height) classes, third line onwards the dbh class and the frequency in the population (number of individuals)Jc correto.txtScenario for Dipteryx odorataThis file contains all parameters (ecological, reproductive and genetic) of Dipterxy odorata for running the Ecogene programdo350 mar09 ecolab.txtGenetic input of Dipterxy odorataThis file consists of the genetic input for running the simulations on Ecogene program. The file contains the number of individuals, coordinates (2 columns), dbh (diameter at breast height) and genotypes of 7 microsatellite markersdo 350 anos.txtMortality data of Dipteryx odorataThis file consists of the mortality data of Jacaranda copaia, the file contains: first line is the header, second line is the number of dbh (diameter at breast height) classes, third line onwards the dbh class and the frequency in the population (number of individuals)cumaru14.txtDemography data of the speciesIn this file contains data of 15 species, including Jacaranda copaia and Dipteryx odorata. The input contais the species name, Mean diameter, SD diameter, Diameter temp. correlation, Max Diameter, Max heighttropical treeschris.txt The impact of logging and subsequent recovery after logging is predicted to vary depending on specific life history traits of the logged species. The Eco-gene simulation model was used to evaluate the long-term impacts of selective logging over 300 years on two contrasting Brazilian Amazon tree species, Dipteryx odorata and Jacaranda copaia. D. odorata (Leguminosae), a slow growing climax tree, occurs at very low densities, whereas J. copaia (Bignoniaceae) is a fast growing pioneer tree that occurs at high densities. Microsatellite multilocus genotypes of the pre-logging populations were used as data inputs for the Eco-gene model and post-logging genetic data was used to verify the output from the simulations. Overall, under current Brazilian forest management regulations, there were neither short nor long-term impacts on J. copaia. By contrast, D. odorata cannot be sustainably logged under current regulations, a sustainable scenario was achieved by increasing the minimum cutting diameter at breast height from 50 to 100 cm over 30-year logging cycles. Genetic parameters were only slightly affected by selective logging, with reductions in the numbers of alleles and single genotypes. In the short term, the loss of alleles seen in J. copaia simulations was the same as in real data, whereas fewer alleles were lost in D. odorata simulations than in the field. The different impacts and periods of recovery for each species support the idea that ecological and genetic information are essential at species, ecological guild or reproductive group levels to help derive sustainable management scenarios for tropical forests.

Dataset underpinning the published article: Resonant Band-Edge Emissive States in Strongly Confined CsPbBr3 Perovskite Nanoplatelets. J. Phys. Chem. C, 2021, . DOI: 10.1021/acs.jpcc.1c01353

In the Neotropical region, euphonias (Euphonia spp., Fringillidae) are the quintessential example of specialized bird frugivores, making the bulk of feeding visits to certain mistletoes (Phoradendron spp., Santalaceae) and epiphytes in the genus Rhipsalis (Cactaceae), whose fruits have high water and low sugar and protein concentrations. Surprisingly, a mechanistic explanation for such specialized, otherwise rare, relationships is lacking. Using captive birds and artificial diets, we contrasted euphonias with frugivorous tanagers in the genus Thraupis (Thraupidae), which rarely eats Rhipsalis fruits, to test the hypothesis that the digestive capacity of euphonias entails them to exploit such low-energy fruits. We expected that compensatory feeding in response to decreasing energy density would occur only in euphonias, whose higher reliance on fruits would entail a lower nitrogen requirement than the tanagers. Euphonias and tanagers were both able to compensate energy intake as sugar density decreased, and both species had the same mass-corrected energy intake at any given sugar concentration. Similarly, euphonias and tanagers did not differ in mass-corrected maintenance nitrogen requirement. Therefore, the physiological traits we investigated do not explain euphonia´s specialization on Rhipsalis fruits. The fast rates of fruit passage typical of specialized avian frugivores as euphonias that entail the processing of a large volume of fruits, and the putative better abilities of such birds to deal with secondary compounds likely present in Rhipsalis fruits are other possible mechanisms that should be considered in future studies to unveil the mechanisms underlying the intriguing specialized relationships between euphonias and certain fruits. Please, refer to the associated article.

This data repository contains sequence alignments, gene trees, species phylogenies, and morphometric data used in the study below: Bravo, G. A. et al. Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi. Ornithology. In press. Specifically, the data contained here is as follows: 1. UCEs_exons_concatenated.phy: FASTA alignment containing concatenated sequences for 2,142 regions flanking UCEs (36 individuals; 1,415,745 bp; average of 661 bp/locus) and 27 exons (36; individuals; 14,484 bp; average of 536 bp/locus) that were used in phylogenomic analyses aiming at assessing generic relationships of the antbird genera Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus. 2. PartitionFile_UCEs_concatenated.txt: Partition file of the FASTA file above to run a partitioned concatenated analysis or separate gene alignments needed for subsequent coalescent-based phylogenetic methods. 3. UCEs_exons_concatenated.tre: Tree file resulting from the partitioned concatenated analysis using RAxML. 4. All_gene_trees.tre: Unrooted gene trees for all 2,169 loci obtained using IQ-TREE. 5. All_gene_trees_no_toepad.tre: Tree file containing 2,169 unrooted gene trees with one toepad sample removed (Herpsilochmus axillaris senex ANSP 158009) to be used in ASTRAL. 6. Astral_notoepad_nobs.tre: Tree file resulting from running ASTRAL. 7. Reduced_genetrees_coalescent_tests.tre: Tree file containing 1,683 gene trees built on a reduced subset of 9 individuals to run coalescent-based tests of alternative genus-level topologies. 8. ND2_all.FASTA: Fasta alignment of the complete mitochondrial gene ND2 (1,041 bp) for 103 thamnophilids. 9. ND2.treefile.tre: Tree file containing ND2 gene tree file obtained using IQ-TREE. 10. Morphometric_data.txt: Tab-delimited file containing raw data for 11 morphological variables (242 individuals) used in multivariate morphometric analyses. Note: This is the same table as Table S2 in the manuscript. Raw UCE and exon data are available at NCBI BioProject PRJNA655842 (See Supplemental Material Table S1 in the manuscript for SRA numbers). The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus and Sakesphorus are not monophyletic. We resolve H. sellowi as a deep-branch sister species to the monotypic genus Biatas and S. cristatus as sister to a clade comprising Herpsilochmus sensu stricto and Dysithamnus. These results are consistent across loci, obtained via concatenation and coalescent-based analyses, and supported by likelihood-ratio tests of the distribution of our sampled coalescent histories. The phenotypic distinctiveness of both H. sellowi and Biatas argues against merging them into a single genus. Because no generic name is available for H. sellowi, we describe a monotypic genus. The polyphyly of Sakesphorus warrants recognition of the available generic name Sakesphoroides for the distinctive and monotypic S. cristatus. Furthermore, we recover six well-supported species groups within Herpsilochmus sensu stricto. Within the context of the family as a whole, the ubiquity of long terminal branches representing monotypic genera points to extinction events among ancestors of these lineages. We suggest that retention of ancestral characters or random genetic drift coupled with extensive extinction could explain the high degree of morphological and ecological similarity across these taxa, but we highlight the potential role of the environment in driving adaptive phenotypic convergence. Finally, our results send a cautionary message against the blind use of phylogenies containing imputed data based on taxonomy due to the increasingly frequent mismatches between traditional taxonomic classification and molecular phylogenies.

Images of village weaver nests- 2008These are the raw images used in our texture analysis of weaverbird nests. Images are of the completed nests of: six Village weavers (Ploceus cucullatus) collected in June and July 2008, from, Laminga Village, Jos, Nigeria. The filename indicates which male build the nest (M), which of that males nests the image is of (N) and which face of the nest the image is of (e.g. front). So an image of the front of Male 1’s, second nest would be: M1N2frontVillage-weaver_2008.zipImages of Southern-masked weaver nests -2008These are the raw images used in our texture analysis of weaverbird nests. 15 Southern Masked weavers (P. velatus) from Botswana (Atholl Holme 11-KO, Gaberone) photographed in November and December 2008. The filename indicates which male build the nest (M), which of that males nests the image is of (N) and which face of the nest the image is of (e.g. front). So an image of the front of Male 1’s, second nest would be: M1N2frontSouthern-masked-weaver_2008.zipImages of Southern-masked weaver nests- 2009These are the raw images used in our texture analysis of weaverbird nests. Images are of the completed nests of 7 Southern Masked weavers (P. velatus) from Botswana (Atholl Holme 11-KO, Gaberone) photographed in November and December 2009. The filename indicates which male build the nest (M), which of that males nests the image is of (N) and which face of the nest the image is of (e.g. front). So an image of the front of Male 1’s, second nest would be: M1N2frontSouthern-masked-weaver_2009.zip In nature, many animals build structures that can be readily measured at the scale of their gross morphology (e.g. length, volume and weight). Capturing individuality as can be done with the structures designed and built by human architects or artists, however, is more challenging. Here, we tested whether computer-aided image texture classification approaches can be used to describe textural variation in the nests of weaverbirds (Ploceus species) in order to attribute nests to the individual weaverbird that built them. We found that a computer-aided texture analysis approach does allow the assignment of a signature to weaverbirds' nests. We suggest that this approach will be a useful tool with which to examine individual variation across a range of animal constructions, not just for nests.

Here, we explore the mating pattern and genetic structure of a tropical tree species, Cariniana estrellensis, in a small population in which progeny arrays (n=399), all adults (n=28) and all seedlings (n=39) were genotyped at nine highly informative microsatellite loci. From progeny arrays we were able to identify the source tree for at least 78% of pollination events. The gene immigration rates, mainly attributable to pollen, were high, varying from 23.5 to 53%. Although gene dispersal over long distance was observed, the effective gene dispersal distances within the small population were relatively short, with mean pollination distances varying from 69.9 to 146.9 m, and seed dispersal distances occurring up to a mean of 119.6 m. Mating system analyses showed that C. estrellensis is an allogamous species (tm=0.999), with both biparental inbreeding (tm−ts=−0.016) and selfing rates (s=0.001) that are not significantly different from zero. Even though the population is small, the presence of private alleles in both seedlings and progeny arrays and the elevated rates of gene immigration indicate that the C. estrellensis population is not genetically isolated. However, genetic diversity expressed by allelic richness was significantly lower in postfragmentation life stages. Although there was a loss of genetic diversity, indicating susceptibility of C. estrellensis to habitat fragmentation, no evidence of inbreeding or spatial genetic structure was observed across generations. Overall, C. estrellensis showed some resilience to negative genetic effects of habitat fragmentation, but conservation strategies are needed to preserve the remaining genetic diversity of this population. SSR genotypes for adults, seedlings and progeny arrays of Cariniana estrellensisGenotypes of Cariniana estrellensis (Lecythidaceae) individuals (adults, seedlings and progeny arrays) based on nine microsatellite loci.SSR_genotypes.xlsx

This is a dataset on benthic diatom communities sampled in 90 riffles (the local communities) within nine near-pristine subtropical streams (each stream represented a metacommunity) in southeast subtropical Brazil. In addition to the dataset, we also provide the R code used to investigate whether reduced enumeration efforts (i.e., subsets of counted valves per sample) and the identification to the genus level are sufficient to recover patterns in the species composition and in beta diversity of benthic diatom metacommunities. This study was partially funded by grant nº 2013/50424-1 from the São Paulo Research Foundation (FAPESP) to TS. ASM and LMB are supported by research grants from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq n° 313954/2021-6 and 308974/2020-4, respectively). EC was supported by a student fellowship by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) – Finance Code 001.