Resumo: Descrevemos de forma resumida resultados selecionados do nosso projeto temático com foco na biodiversidade da Floresta Atlântica (“AF BIOTA”), que foi financiado pelo BIOTA FAPESP e pelo programa “Dimensions of Biodiversity” da “U.S. National Science Foundation” e “National Aeronautics and Space Administration” (NASA). Devido à sua megabiodiversidade (que inclui várias espécies endêmicas), e por restar menos de 16% da vegetação original, a Floresta Atlântica (FA) é uma das cinco áreas mais importantes para a biodiversidade do planeta (“biodiversity hotspot”). Reunimos especialistas de diversas disciplinas (biologia, geologia, engenharia) visando compreender como essa megabiodiversidade evoluiu ao longo do tempo e fornecer informações científicas para a sua conservação. Dentre os resultados obtidos, nós formamos 18 mestres e 26 doutores, publicamos mais de 400 artigos científicos que aumentaram o conhecimento sobre a diversidade biológica e climática da FA e sua dinâmica ao longo do tempo, desenvolvemos novos métodos analíticos, produzimos material de divulgação científica e fornecemos dados para desenvolver políticas públicas de conservação da biodiversidade.

Abstract: We briefly describe selected results from our thematic project focused on the biodiversity of the Atlantic Forest (“AF BIOTA”), which was jointly funded by FAPESP’s BIOTA Program, the U.S. National Science Foundation Dimensions of Biodiversity Program, and the National Aeronautics and Space Administration (NASA). As one of the five most important hotspots of biodiversity in the world, the Atlantic Forest (AF) holds less than 16% of its vegetation cover, yet, amongst the hotspots, it still harbors one of the highest numbers of species, including endemics. By gathering specialists across multiple disciplines (biology, geology, engineering), we aimed to understand how this megabiodiversity was built through time, informing biodiversity science and conservation. Among the results, we trained 18 Master’s and 26 Ph.D. students, published more than 400 peer-reviewed papers that improved our knowledge about the forest’s biologic and climatic diversity and dynamics through time, developed new analytical methods, produced outreach videos and articles, and provided data to help define biodiversity conservation policies.

Abstract Amazon parrots are long-lived birds with highly developed cognitive skills, including vocal learning. Several parrot mitogenomes have been sequenced, but important aspects of their organization and evolution are not fully understood or have limited experimental support. The main aim of the present study was to describe the mitogenome of the blue-fronted Amazon, Amazona aestiva, and compare it to other mitogenomes from the genus Amazona and the order Psittaciformes. We observed that mitogenomes are highly conserved among Amazon parrots, and a detailed analysis of their duplicated control regions revealed conserved blocks. Population level analyses indicated that the specimen analyzed here seems to be close to A. aestiva individuals from Bahia state. Evolutionary relationships of 41 Psittaciformes species and three outgroups were inferred by BEAST. All relationships were retrieved with high support.

Molted feather sampling is a useful tool for genetic analyses of endangered species, but it is often very laborious due to the low quality and quantity of the DNA obtained. In the present study we show the parts of feathers that resulted in better yield of DNA. In descending order these were: blood clot outside the umbilicus, umbilicus (without blood clot), tip, inner membrane, and small calamus. Compared to DNA extracted from blood samples, DNA extracted from feathers produced microsatellite alleles of poorer quality and had to be processed immediately after extraction. As expected due to the level of DNA degradation, molecular sexing protocols that result in shorter PCR products were more efficient.

Cross-amplification was tested and variability in microsatellite primers (designed for Neotropical parrots) compared, in five macaw species, viz., three endangered blue macaws (Cyanopsitta spixii [extinct in the wild], Anodorhynchus leari [endangered] and Anodorhynchus hyacinthinus [vulnerable]), and two unthreatened red macaws (Ara chloropterus and Ara macao). Among the primers tested, 84.6% successfully amplified products in C. spixii, 83.3% in A. leari, 76.4% in A. hyacinthinus, 78.6% in A. chloropterus and 71.4% in A. macao. The mean expected heterozygosity estimated for each species, and based on loci analyzed in all the five, ranged from 0.33 (A. hyacinthinus) to 0.85 (A. macao). As expected, the results revealed lower levels of genetic variability in threatened macaw species than in unthreatened. The low combined probability of genetic identity and the moderate to high potential for paternity exclusion, indicate the utility of the microsatellite loci set selected for each macaw species in kinship and population studies, thus constituting an aid in planning in-situ and ex-situ conservation.

More than 90% of birds are socially monogamous, although genetic studies indicate that many are often not sexually monogamous. In the present study, DNA fingerprinting was used to estimate the genetic relationships between nestlings belonging to the same broods to evaluate the mating system in the socially monogamous macaw, Ara ararauna. We found that in 10 of 11 broods investigated, the nestlings showed genetic similarity levels congruent with values expected among full-sibs, suggesting that they shared the same parents. However, in one brood, the low genetic similarity observed between nestlings could be a result of intraspecific brood parasitism, intraspecific nest competition or extra-pair paternity. These results, along with available behavioral and life-history data, imply that the blue-and-yellow macaw is not only socially, but also genetically monogamous. However, the occurrence of eventual cases of extra-pair paternity cannot be excluded.

The selection of molecular markers for population studies is an important tool for biodiversity conservation. The family Psittacidae contains many endangered and vulnerable species and we tested three kinds of molecular markers for their potential use in population studies of five psitacid species: 43 hyacinth macaws (Anodorhynchus hyacinthinus), 42 blue-and-yellow macaws (Ara ararauna), 23 red-and-green macaws (Ara chloroptera), 19 red-spectacled amazons (Amazona pretrei); and 18 red-tailed amazons (Amazona brasiliensis). We tested 21 clones from a genomic library of golden conure (Guarouba guarouba) minisatellites and 12 pairs of microsatellite primers developed for the domestic chicken (Gallus gallus) and A. hyacinthinus. We also tested seven tetranucleotide repeat primers for their ability to amplify regions between microsatellite loci (inter simple sequence repeats, ISSRs). We were able to select seven markers that were variable in different degrees for three species (A. hyacinthinus, A. chloroptera and A. ararauna). The mini and microsatellites produced more polymorphic patterns than the ISSRs. The genetic variability of the species studied seems to be correlated with their endangered status.