Introducing the biogeographic species pool

The species pool concept has played a central role in the development of ecological theory for at least 60 yr. Surprisingly, there is little consensus as to how one should define the species pool, and consequently, no systematic approach exists. Because the definition of the species pool is essential to infer the processes that shape ecological communities, there is a strong incentive to develop an ecologically realistic definition of the species pool based on repeatable and transparent analytical approaches. Recently, several methodological tools have become available to summarize repeated patterns in the geographic distribution of species, phylogenetic clades and taxonomically broad lineages. Here, we present three analytical approaches that can be used to define what we term 'the biogeographic species pool': distance-based clustering analysis, network modularity analysis, and assemblage dispersion fields. The biogeographic species pool defines the pool of potential community members in a broad sense and represents a first step towards a standardized definition of the species pool for the purpose of comparative ecological, evolutionary and biogeographic studies. © 2013 The Authors.

Variabilidade espacial e correlações entre atributos de solo e produtividade na agricultura de precisão

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Utilização de técnicas multivariadas na avaliação da divergência genética de populações de girassol (Helianthus annuus L.)

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Produção de folhas, óleo essencial e anatomia foliar quantitativa de Lippia alba (Mill.) N.E.Br. (Verbenaceae) em diferentes níveis de sombreamento e épocas de colheita

Pós-graduação em Agronomia (Horticultura) - FCA

Análise espacial e temporal de atributos do solo e da produtividade das culturas visando manejo específico em áreas agrícolas

Pós-graduação em Agronomia (Produção Vegetal) - FCAV

Foraminifera, thecamoebians and palynomorphs as hydrodynamic indicators in Araguari Estuary, Amazonian Coast, Amapá State - Brazil

O regime de macromaré e a pororoca controlam a dinâmica estuarina do Araguari, na qual é muito diferente dos modelos tradicionais dos estuários sob este regime de maré. Objetivando estabelecer zonas estuarinas no Araguari com base em assembléias de foraminíferos, tecamebas, palinomorfos e parâmetros físico-químicos, foram estabelecidas dezesseis estações amostrais ao longo do estuário. A turbidez e a temperatura foram os parâmetros ambientais que permitiram determinar gradiente estuarino. Dezoito espécies de foraminíferos, dez espécies de tecamebas e quatorze espécies de palinomorfos foram identificadas. A análise de agrupamento em modo-R mostrou a existência de assembléias de foraminíferos e quatro de palinomorfos. A análise em CCA demonstrou que a turbidez e a matéria orgânica como os parâmetros de maior influência na distribuição dos foraminíferos tecamebas no Araguari. A análise de agrupamento em Modo-Q usando todos os dados formou quarto grupos de estações que sugerem a existência de três zonas estuarinas: Zona I - composta por tecamebas e palinomorfos continentais; Zona II - compostas por foraminíferos de manguezal, acritacos e todas as assembléias de palinomorfos; e Zona III - composta por foraminíferos de manguezal e estuarinos e por todas as assembléias de palinomorfos.

Cryptic Genetic Diversity Is Paramount in Small-Bodied Amphibians of the Genus Euparkerella (Anura: Craugastoridae) Endemic to the Brazilian Atlantic Forest

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A mathematical approach to simulate spatio-temporal patterns of an insect-pest, the corn rootworm Diabrotica speciosa (Coleoptera: Chrysomelidae) in intercropping systems

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic diversity and population structure of the New World screwworm fly from the Amazon region of Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Long-term clinical evaluation of the color stability and stainability of acrylic resin denture teeth

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Filogeografia do complexo Ischnocnema lactea e Ischnocnema holti (Anura, Brachycephalidae), sudeste do Brasil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Population divergence of Melipona scutellaris (Hymenoptera: Meliponina) in two restricted areas in Bahia, Brazil

Melipona scutellaris Latreille has great economic and ecological importance, especially because it is a pollinator of native plant species. Despite the importance of this species, there is little information about the conservation status of their populations. The objective of this study was to assess the diversity in populations of M. scutellaris coming from a Semideciduous Forest Fragment and an Atlantic Forest Fragment in the Northeast Brazil, through geometric morphometric analysis of wings in worker bees. In each area, worker bees were collected from 10 colonies, 10 workers per colony. To assess the diversity on the right wings of worker bees, 15 landmarks were plotted and the measures were used in analysis of variance and multivariate analysis, principal component analysis, discriminant analysis and clustering analysis. There were significant differences in the shape of the wing venation patterns between colonies of two sites (Wilk's lambda = 0.000006; p < 0.000001), which is probably due to the geographical distance between places of origin which impedes the gene flow between them. It indicates that inter and intrapopulation morphometric variability exists (p < 0.000001) in M. scutellaris coming from two different biomes, revealing the existence of diversity in these populations, which is necessary for the conservation of this bee species.

Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida) is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (similar to 150 Mb). Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi) were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia) and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas) compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST) indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome.

Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera

Abstract Background Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1-related sequences in 20 wild species of Solanum and five cultivars of Solanum tuberosum. Results Tnt1-related sequences were amplified from total genomic DNA using a PCR-based approach. Purified fragments were cloned and sequenced, and clustering analysis revealed three groups that differ in their U3 region. Using a network approach with a total of 453 non-redundant sequences isolated from Solanum (197), Nicotiana (140) and Lycopersicon (116) species, it is demonstrated that the Tnt1 superfamily can be treated as a population to resolve previous phylogenetic multifurcations. The resulting RNAseH network revealed that sequences group according to the Solanaceae genus, supporting a strong association with the host genome, whereas tracing the U3 region sequence association characterises the modular evolutionary pattern within the Tnt1 superfamily. Within each genus, and irrespective of species, nearly 20% of Tnt1 sequences analysed are identical, indicative of being part of an active copy. The network approach enabled the identification of putative "master" sequences and provided evidence that within a genus these master sequences are associated with distinct U3 regions. Conclusion The results presented here support the hypothesis that the Tnt1 superfamily was present early in the evolution of Solanaceae. The evidence also suggests that the RNAseH region of Tnt1 became fixed at the host genus level whereas, within each genus, propagation was ensured by the diversification of the U3 region. Different selection pressures seemed to have acted on the U3 and RNAseH modules of ancestral Tnt1 elements, probably due to the distinct functions of these regions in the retrotransposon life cycle, resulting in both co evolution and adaptation of the element population with its host.

Genetic diversity and population structure of Musa accessions in ex situ conservation

Abstract Background Banana cultivars are mostly derived from hybridization between wild diploid subspecies of Musa acuminata (A genome) and M. balbisiana (B genome), and they exhibit various levels of ploidy and genomic constitution. The Embrapa ex situ Musa collection contains over 220 accessions, of which only a few have been genetically characterized. Knowledge regarding the genetic relationships and diversity between modern cultivars and wild relatives would assist in conservation and breeding strategies. Our objectives were to determine the genomic constitution based on Internal Transcribed Spacer (ITS) regions polymorphism and the ploidy of all accessions by flow cytometry and to investigate the population structure of the collection using Simple Sequence Repeat (SSR) loci as co-dominant markers based on Structure software, not previously performed in Musa. Results From the 221 accessions analyzed by flow cytometry, the correct ploidy was confirmed or established for 212 (95.9%), whereas digestion of the ITS region confirmed the genomic constitution of 209 (94.6%). Neighbor-joining clustering analysis derived from SSR binary data allowed the detection of two major groups, essentially distinguished by the presence or absence of the B genome, while subgroups were formed according to the genomic composition and commercial classification. The co-dominant nature of SSR was explored to analyze the structure of the population based on a Bayesian approach, detecting 21 subpopulations. Most of the subpopulations were in agreement with the clustering analysis. Conclusions The data generated by flow cytometry, ITS and SSR supported the hypothesis about the occurrence of homeologue recombination between A and B genomes, leading to discrepancies in the number of sets or portions from each parental genome. These phenomenons have been largely disregarded in the evolution of banana, as the “single-step domestication” hypothesis had long predominated. These findings will have an impact in future breeding approaches. Structure analysis enabled the efficient detection of ancestry of recently developed tetraploid hybrids by breeding programs, and for some triploids. However, for the main commercial subgroups, Structure appeared to be less efficient to detect the ancestry in diploid groups, possibly due to sampling restrictions. The possibility of inferring the membership among accessions to correct the effects of genetic structure opens possibilities for its use in marker-assisted selection by association mapping.