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1.  Recovering species demographic history from multi-model inference: the case of a Neotropical savanna tree species 
BMC Evolutionary Biology  2014;14(1):213.
Background
Glaciations were recurrent throughout the Quaternary and potentially shaped species genetic structure worldwide by affecting population dynamics. Here, we implemented a multi-model inference approach to recover the distribution dynamics and demographic history of a Neotropical savanna tree, Tabebuia aurea (Bignoniaceae). Exploring different algorithms and paleoclimatic simulations, we used ecological niche modelling to generate alternative hypotheses of potential demographic changes through the last glacial cycle and estimated genetic parameters using coalescent modelling.
Results
Comparing predictions from demographic hypotheses with genetic parameters of modern populations, our findings revealed a likely scenario of population decline, with spatial displacement towards Northeast Brazil from the last glacial maximum to the mid-Holocene. Subsequently, populations expanded in response to the return of the climatically suitable conditions in Central-West Brazil. Nevertheless, a wide historical refugium across Central Brazil likely maintained large populations connected throughout time. The expected genetic signatures from such predicted distribution dynamics are also corroborated by spatial genetic structure observed in modern populations.
Conclusion
By exploring uncertainties inherent in multiple working hypotheses, we have shown that multi-model inference is a fruitful and efficient approach to recover the nature, timing and geographical context of the Tabebuia aurea population dynamic in response to the Quaternary climate changes.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-014-0213-0) contains supplementary material, which is available to authorized users.
doi:10.1186/s12862-014-0213-0
PMCID: PMC4205293  PMID: 25301477
Coalescent simulation; Ecological niche modelling; Genetic connectivity; Habitat tracking; Multiple working hypotheses; Quaternary climate changes
3.  Effects of Genetic Variability and Habitat of Qualea parviflora (Vochysiaceae) on Herbivory by Free-feeding and Gall-forming Insects 
Annals of Botany  2004;94(2):259-268.
• Background and Aims Differences in the chemical and physical traits of plants caused by both genetic and habitat characteristics may influence attack by herbivores. Leaves of Qualea parviflora (Vochysiaceae), a common tree of different habitats in the Brazilian Neotropical savannas (cerrado), are susceptible to severe attack by herbivorous free-living and gall-forming insects. Attack by free-living and gall-forming insects within and between populations of Q. parviflora were examined and it was determined to what extent genetic variability (detected by RAPD markers), phenotypic characteristics of the plants and habit traits influence the number of free-living and gall-forming insect species and individuals attacking the plants, and the intensity of attack.
• Methods On four occasions in 2000, leaves were sampled from ten individual trees in each of three types of vegetation in the cerrado: campo sujo, cerrado sensu stricto and cerradão at the Ecological Station of Pirapitinga (ESP), in Três Marias, north-western Minas Gerais, Brazil. Genetic variability was detected by RAPD markers, and concentrations of nutrients, phenols and tannins, sclerophylly and pre-dawn water potential of leaves were measured. Water and nutrient contents in the soil below each tree characterized the habitat. The free-living and gall-forming herbivorous insects were determined.
• Key Results Of 69 RAPD markers analysed, 41 were polymorphic and were used for analyses of genetic variability of Q. parviflora. Most of the variability occurred within habitats, accounting for 97·65 % of the genetic variability. Plants in the cerrado sensu stricto and campo sujo were the most similar. There were no significant associations between genetic similarity and the chemical and physical traits of Q. parviflora, or with habitat, nor was there significant correlation between phenotypic and habitat traits. Increasing concentrations of tannins and sulphur, C : N ratio and sclerophylly correlated with increasing percentage of leaf area damaged by herbivores. Decreased sclerophylly, concentration of tannins and C : N ratio, and increased concentration of nutrients in leaves correlated with increased severity of attack by gall-forming insects.
• Conclusions Nutrient concentration in the soil had more influence, indirectly, on free-feeding insects than did composition of Q. parviflora leaves. However, gall-forming insects are affected more by leaf quality, attacking fewer sclerophyllous leaves, with larger nutrient but smaller tannin concentrations.
doi:10.1093/aob/mch136
PMCID: PMC4242161  PMID: 15234928
Cerrado; genetic variability; gall attack; herbivory; insect galls; plant quality; Qualea parviflora; RAPD; Vochysiaceae
4.  Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae†  
Vasconcelos, Ana Tereza R. | Ferreira, Henrique B. | Bizarro, Cristiano V. | Bonatto, Sandro L. | Carvalho, Marcos O. | Pinto, Paulo M. | Almeida, Darcy F. | Almeida, Luiz G. P. | Almeida, Rosana | Alves-Filho, Leonardo | Assunção, Enedina N. | Azevedo, Vasco A. C. | Bogo, Maurício R. | Brigido, Marcelo M. | Brocchi, Marcelo | Burity, Helio A. | Camargo, Anamaria A. | Camargo, Sandro S. | Carepo, Marta S. | Carraro, Dirce M. | de Mattos Cascardo, Júlio C. | Castro, Luiza A. | Cavalcanti, Gisele | Chemale, Gustavo | Collevatti, Rosane G. | Cunha, Cristina W. | Dallagiovanna, Bruno | Dambrós, Bibiana P. | Dellagostin, Odir A. | Falcão, Clarissa | Fantinatti-Garboggini, Fabiana | Felipe, Maria S. S. | Fiorentin, Laurimar | Franco, Gloria R. | Freitas, Nara S. A. | Frías, Diego | Grangeiro, Thalles B. | Grisard, Edmundo C. | Guimarães, Claudia T. | Hungria, Mariangela | Jardim, Sílvia N. | Krieger, Marco A. | Laurino, Jomar P. | Lima, Lucymara F. A. | Lopes, Maryellen I. | Loreto, Élgion L. S. | Madeira, Humberto M. F. | Manfio, Gilson P. | Maranhão, Andrea Q. | Martinkovics, Christyanne T. | Medeiros, Sílvia R. B. | Moreira, Miguel A. M. | Neiva, Márcia | Ramalho-Neto, Cicero E. | Nicolás, Marisa F. | Oliveira, Sergio C. | Paixão, Roger F. C. | Pedrosa, Fábio O. | Pena, Sérgio D. J. | Pereira, Maristela | Pereira-Ferrari, Lilian | Piffer, Itamar | Pinto, Luciano S. | Potrich, Deise P. | Salim, Anna C. M. | Santos, Fabrício R. | Schmitt, Renata | Schneider, Maria P. C. | Schrank, Augusto | Schrank, Irene S. | Schuck, Adriana F. | Seuanez, Hector N. | Silva, Denise W. | Silva, Rosane | Silva, Sérgio C. | Soares, Célia M. A. | Souza, Kelly R. L. | Souza, Rangel C. | Staats, Charley C. | Steffens, Maria B. R. | Teixeira, Santuza M. R. | Urmenyi, Turan P. | Vainstein, Marilene H. | Zuccherato, Luciana W. | Simpson, Andrew J. G. | Zaha, Arnaldo
Journal of Bacteriology  2005;187(16):5568-5577.
This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen Mycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in the M. hyopneumoniae strains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences from M. gallisepticum to M. synoviae.
doi:10.1128/JB.187.16.5568-5577.2005
PMCID: PMC1196056  PMID: 16077101

Results 1-4 (4)