Structure, diversity, and spatial patterns in a permanent plot of a high Restinga forest in Southeastern Brazil

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

Genetic diversity strategy for the management and use of rubber genetic resources: more than 1,000 wild and cultivated accessions in a 100-genotype core collection

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

Influence of removal of a non-native tree species Mimosa caesalpiniifolia Benth. on the regenerating plant communities in a tropical semideciduous forest under restoration in Brazil

Exotic species are used to trigger facilitation in restoration plantings, but this positive effect may not be permanent and these species may have negative effects later on. Since such species can provide a marketable product (firewood), their harvest may represent an advantageous strategy to achieve both ecological and economic benefits. In this study, we looked at the effect of removal of a non-native tree species (Mimosa caesalpiniifolia) on the understory of a semideciduous forest undergoing restoration. We assessed two 14-year-old plantation systems (modified taungya agroforestry system; and mixed plantation using commercial timber and firewood tree species) established at two sites with contrasting soil properties in São Paulo state, Brazil. The experimental design included randomized blocks with split plots. The natural regeneration of woody species (height ≥0.2 m) was compared between managed (all M. caesalpiniifolia trees removed) and unmanaged plots during the first year after the intervention. The removal of M. caesalpiniifolia increased species diversity but decreased stand basal area. Nevertheless, the basal area loss was recovered after 1 year. The management treatment affected tree species regeneration differently between species groups. The results of this study suggest that removal of M. caesalpiniifolia benefited the understory and possibly accelerated the succession process. Further monitoring studies are needed to evaluate the longer term effects on stand structure and composition. The lack of negative effects of tree removal on the natural regeneration indicates that such interventions can be recommended, especially considering the expectations of economic revenues from tree harvesting in restoration plantings.

Genetic characterization of fig tree mutants with molecular markers

The fig (Ficus carica L.) is a fruit tree of great world importance and, therefore, the genetic improvement becomes an important field of research for better crops, being necessary to gather information on this species, mainly regarding its genetic variability so that appropriate propagation projects and management are made. The improvement programs of fig trees using conventional procedures in order to obtain new cultivars are rare in many countries, such as Brazil, especially due to the little genetic variability and to the difficulties in obtaining plants from gamete fusion once the wasp Blastophaga psenes, responsible for the natural pollinating, is not found in Brazil. In this way, the mutagenic genetic improvement becomes a solution of it. For this reason, in an experiment conducted earlier, fig plants formed by cuttings treated with gamma ray were selected based on their agronomic characteristics of interest. We determined the genetic variability in these fig tree selections, using RAPD and AFLP molecular markers, comparing them to each other and to the Roxo-de-Valinhos, used as the standard. For the reactions of DNA amplification, 140 RAPD primers and 12 primer combinations for AFLP analysis were used. The selections did not differ genetically between themselves and between them and the Roxo-de-Valinhos cultivar. Techniques that can detect polymorphism between treatments, such as DNA sequencing, must be tested. The phenotypic variation of plants may be due to epigenetic variation, necessitating the use of techniques with methylation-sensitive restriction enzymes.

Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America's open biomes

The gecko genus Phyllopezus occurs across South America's open biomes: Cerrado, Seasonally Dry Tropical Forests (SDTF, including Caatinga), and Chaco. We generated a multi-gene dataset and estimated phylogenetic relationships among described Phyllopezus taxa and related species. We included exemplars from both described Phyllopezus pollicaris subspecies, P. p. pollicaris and P. p. przewalskii. Phylogenies from the concatenated data as well as species trees constructed from individual gene trees were largely congruent. All phylogeny reconstruction methods showed Bogertia lutzae as the sister species of Phyllopezus maranjonensis, rendering Phyllopezus paraphyletic. We synonymized the monotypic genus Bogertia with Phyllopezus to maintain a taxonomy that is isomorphic with phylogenetic history. We recovered multiple, deeply divergent, cryptic lineages within P. pollicaris. These cryptic lineages possessed mtDNA distances equivalent to distances among other gekkotan sister taxa. Described P. pollicaris subspecies are not reciprocally monophyletic and current subspecific taxonomy does not accurately reflect evolutionary relationships among cryptic lineages. We highlight the conservation significance of these results in light of the ongoing habitat loss in South America's open biomes. (C) 2011 Elsevier Inc. All rights reserved.

Cyanobacterial diversity in the phyllosphere of a mangrove forest

The cyanobacterial community colonizing phyllosphere in a well-preserved Brazilian mangrove ecosystem was assessed using cultivation-independent molecular approaches. Leaves of trees that occupy this environment (Rhizophora mangle, Avicennia schaueriana and Laguncularia racemosa) were collected along a transect beginning at the margin of the bay and extending upland. The results demonstrated that the phyllosphere of R.similar to mangle and L.similar to racemosa harbor similar assemblages of cyanobacteria at each point along the transect. A.similar to schaueriana, found only in the coastal portions of the transect, was colonized by assemblages with lower richness than the other trees. However, the results indicated that spatial location was a stronger driver of cyanobacterial community composition than plant species. Distinct cyanobacterial communities were observed at each location along the coast-to-upland transect. Clone library analysis allowed identification of 19 genera of cyanobacteria and demonstrated the presence of several uncultivated taxa. A predominance of sequences affiliated with the orders Nostocales and Oscillatoriales was observed, with a remarkable number of sequences similar to genera Symphyonemopsis/Brasilonema (order Nostocales). The results demonstrated that phyllosphere cyanobacteria in this mangrove forest ecosystem are influenced by environmental conditions as the primary driver at the ecosystem scale, with tree species exerting some effect on community structure at the local scale.

Two new species of marsupial tree-frogs genus Gastrotheca Fitzinger, 1843 (Anura, Hemiphractidae) from the Brazilian Atlantic Forest

Two new species of Gastrotheca are described from northeastern Minas Gerais and southern Bahia, in the Atlantic Forest of Brazil. Data on morphology, calls, mitochondrial, and nuclear DNA are provided. Allied to G. fissipes and G. megacephala, the new taxa provide evidence for a higher diversity of species of Gastrotheca than previously thought at the Atlantic Forest. The data also suggest that G. pulchra, another Atlantic Forest taxon, is more closely related to non-Atlantic Forest species than to the remaining analyzed Brazilian Gastrotheca species. This implies that the Gastrotheca at the Brazilian coastal forests have at least two independent origins.

Genetic diversity of Metrodorea nigra (Rutaceae) from a small forest remnant in Brazil assessed with microsatellite markers

Metrodorea nigra (Rutaceae) is an endemic Brazilian tree of great ecological importance, frequently found in the submontane regions of ombrophilous dense and semideciduous forests. This tree is useful for reforesting degraded areas and the wood can be employed in construction. We developed 12 microsatellite markers from a genomic library enriched for GA/CA repeats, for this species. Polymorphisms were assessed in 40 trees of a highly fragmented population found in Cravinhos, State of Sao Paulo, in southeastern Brazil. Among the 12 loci, 8 were polymorphic and only one had fixed alleles in this population. The number of alleles per locus and expected heterozygosity ranged from 2 to 11 and from 0.190 to 0.889, respectively. These results revealed moderate levels of genetic variation in M. nigra population when compared to other tropical species. Additionally, transferability of the 12 primers was tested in seven other Brazilian Rutaceae tree species (endemics: M. stipularis, Galipea jasminiflora, Esenbeckia leiocarpa and non-endemics: E. febrifuga, E. grandiflora, Balfourodendron riedelianum, Zanthoxylum riedelianum). Transferability ranged among species, but at least 8 loci (similar to 67%) amplified in M. stipularis, demonstrating a high potential for transferring microsatellite markers between species of the same genus in the Rutaceae family.

Responses of transplanted native tree species to invasive alien grass removals in an abandoned cattle pasture in the Lacandon region, Mexico

We tested the early performance of 16 native early-, mid-, and late-successional tree species in response to four intensities of grass removal in an abandoned cattle pasture dominated by the introduced, invasive African grass, Cynodon plectostachyus, within the Lacandon rainforest region, southeast Mexico. The increase in grass removals significantly improved the performance of many species, especially of early-and mid-successional species, while performance of late-successional species was relatively poor and did not differ significantly among treatments. Good site preparation and at least one additional grass removal four months after seedling transplant were found to be essential; additional grass removals led to improved significantly performance of saplings in most cases. In order to evaluate the potential of transplanting tree seedlings successfully in abandoned tropical pastures, we developed a "planting risk index", combining field performance measurements and plantation cost estimations. Our results showed a great potential for establishing restoration plantings with many early-and mid-successional species. Although planting risk of late-successional species was considered high, certain species showed some possibilities of acclimation after 18 months and should be considered in future plantation arrangements in view of their long-term contributions to biodiversity maintenance and also to human welfare through delivery of ecosystem services. Conducting a planting risk analysis can help avoid failure of restoration strategies involving simultaneous planting of early-, mid-, and late-successional tree species. This in turn will improve cost-effectiveness of initial interventions in large-scale, long-term restoration programs.

Testing the Performance of Fourteen Native Tropical Tree Species in Two Abandoned Pastures of the Lacandon Rainforest Region of Chiapas, Mexico

The rainforest of Mexico has been degraded and severely fragmented, and urgently require restoration. However, the practice of restoration has been limited by the lack of species-specific data on survival and growth responses to local environmental variation. This study explores the differential performance of 14 wet tropical early-, mid- or late-successional tree species that were grown in two abandoned pastures with contrasting land-use histories. After 18 months, seedling survival and growth of at least 7 of the 14 tree species studied were significantly higher in the site with a much longer history of land use (site 2). Saplings of the three early-successional species showed exceptional growth rates. However, differences in performance were noted in relation to the differential soil properties between the experimental sites. Mid-successional species generally showed slow growth rates but high seedling survival, whereas late-successional species exhibited poor seedling survival at both the study sites. Stepwise linear regressions revealed that the species integrated response index combining survivorship and growth measurements, was influenced mostly by differences in soil pH between the two abandoned pastures. Our results suggest that local environmental variation among abandoned pastures of contrasting land-use histories influences sapling survival and growth. Furthermore, the similarity of responses among species with the same successional status allowed us to make some preliminary site and species-specific silvicultural recommendations. Future field experiments should extend the number of species and the range of environmental conditions to identify site generalists or more narrowly adapted species, that we would call sensitive.

DEVELOPMENT OF MICROSATELLITE MARKERS FOR ANADENANTHERA COLUBRINA (LEGUMINOSAE), A NEOTROPICAL TREE SPECIES

Premise of the study: We developed and characterized nuclear microsatellite markers for Anadenanthera colubrina, a tropical tree species widely distributed in South America. Methods and Results: Leaf samples of mature A. colubrina trees, popularly called "angico," were collected from an area that is greatly impacted by agricultural practices in the region of Ribeirao Preto in Sao Paulo State in southeastern Brazil. Twenty simple sequence repeat (SSR) markers were developed, 14 of which had polymorphic loci. A total of 96 alleles were detected with an average of 6.86 alleles per polymorphic locus. The expected heterozygosity, calculated at polymorphic loci, ranged from 0.18 to 0.83. Finally, we demonstrated that 18 loci were cross-amplified in A. peregrina. Conclusions: A total of 14 polymorphic markers suggest a high potential for genetic diversity, gene flow, and mating system analyses in A. colubrina.

Diversity and genetic structure in natural populations of Hancornia speciosa var. speciosa Gomes in northeastern Brazil

Hancornia speciosa Gomes is a fruit tree native from Brazil that belongs to Apocinaceae family, and is popularly known as Mangabeira. Its fruits are widely consumed raw or processed as fruit jam, juices and ice creams, which have made it a target of intense exploitation. The extractive activities and intense human activity on the environment of natural occurrence of H. speciosa has caused genetic erosion in the species and little is known about the ecology or genetic structure of natural populations. The objective of this research was the evaluation of the genetic diversity and genetic structure of H. speciosa var. speciosa. The genetic variability was assessed using 11 allozyme loci with a sample of 164 individuals distributed in six natural populations located in the States of Pernambuco and Alagoas, Northeastern Brazil. The results showed a high level of genetic diversity within the species (e= 0.36) seeing that the most of the genetic variability of H. speciosa var. speciosa is within its natural populations with low difference among populations ( or = 0.081). The inbreeding values within ( = -0.555) and among populations ( =-0.428) were low showing lacking of endogamy and a surplus of heterozygotes. The estimated gene flow ( m ) was high, ranging from 2.20 to 13.18, indicating to be enough to prevent the effects of genetic drift and genetic differentiation among populations. The multivariate analyses indicated that there is a relationship between genetic and geographical distances, which was confirmed by a spatial pattern analysis using Mantel test (r = 0.3598; p = 0.0920) with 1000 random permutations. The high genetic diversity index in these populations indicates potential for in situ genetic conservation.

Molecular diversity of Primula apennina and phylogeny of Primula Subsection Euauricula

Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations representative of the species distribution range. High levels of genetic diversity were revealed both at population (PPB = 75.92%, HS = 0.204, Hpop = 0.319) and at species level (PPB = 96.95%, HT = 0.242, Hsp = 0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level of interpopulation diversity. Principal coordinate and bayesian analyses clustered the populations in three major groups along a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r = 0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures are suggested based on the observed pattern of genetic variability. P. apennina belongs to Primula subsect. Euauricula which includes 15 species distributed on the whole Alps and Apennines. A phylogenetic analysis was carried out using AFLP markers in order both to clarify the relationships among the species of subsection Euauricula that remained unresolved in previous works and to make some hypoteses on their evolutive dynamics. NJ, PCO and BAPS analyses strongly confirmed the monophyly of P. subsect. Euauricula and all the species form strongly supported clades. NJ tree topology suggested a simultaneous fragmentations of ancestral species in a large number of isolated populations that survived in refugia along the unglaciated margins of the Alps in response to the Pleistocene climatic oscillations.

Impact of forest fragmentation and disturbance on the endangered tropical tree Prunus africana (Rosaceae)

Anthropogene Fragmentierung und Störung von Wäldern beeinflussen ökologische Prozesse. Darüber hinaus werden genetische Drift und Inzucht verstärkt und die Fitness von Populationen beeinträchtigt. Um die Einflüsse von Fragmentierung und Störung auf die Biodiversität und Prozesse in tropischen Wäldern zu ermitteln, habe ich im „Kakamega Forest“, West-Kenia, die Baumart Prunus africana genauer untersucht. Dabei lag der Fokus auf (i) der Frugivorengemeinschaft und Samenausbreitung, (ii) der Kleinsäugergemeinschaft im Kontext der Samenprädation und (iii) der genetische Populationsstruktur von Keimlingen und adulten Bäumen. Der Vergleich von Keimlingen mit adulten Bäumen ermöglicht es, Veränderungen im Genfluss zwischen Generationen festzustellen. Die Ergebnisse zeigten, dass im untersuchten Waldgebiet insgesamt 49 frugivore Arten (Affen und Vögel) vorkommen. Dabei lag die Gesamtartenzahl im zusammenhängenden Wald höher als in den isoliert liegenden Fragmenten. An den Früchten von P. africana konnten insgesamt 36 Arten fressend beobachtet werden. Hier jedoch wurden in Fragmenten eine leicht erhöhte Frugivorenzahl sowie marginal signifikant erhöhte Samenausbreitungsraten nachgewiesen. Der Vergleich von stark gestörten mit weniger gestörten Flächen zeigte eine höhere Gesamtartenzahl sowie eine signifikant höhere Frugivorenzahl in P. africana in stark gestörten Flächen. Entsprechend war die Samenausbreitungsrate in stark gestörten Flächen marginal signifikant erhöht. Diese Ergebnisse deuten darauf hin, dass die quantitative Samenausbreitung in fragmentierten und gestörten Flächen etwas erhöht ist und somit eine gewisse Artenredundanz besteht, die den Verlust einzelner Arten ausgleichen könnte. Prunus africana Samen, die auf dem Boden lagen, wurden hauptsächlich von einer Nagerart (Praomys cf. jacksonii) erbeutet. Dabei war in gestörten Waldbereichen eine tendenziell höhere Prädatoraktivität zu beobachten als in weniger gestörten. Zudem waren einzelne Samen im Gegensatz zu Samengruppen in gestörten Flächen signifikant höherem Prädationsdruck ausgesetzt. Diese Ergebnisse zeigen, dass Fragmentierung sowie anthropogene Störungen auf unterschiedliche Prozesse im Lebenszyklus eines tropischen Baumes gegensätzliche Effekte haben können. Eine Extrapolation von einem auf einen anderen Prozess kann somit nicht erfolgen. Die genetische Differenzierung der adulten Baumpopulationen war gering (FST = 0.026). Der Großteil ihrer Variation (~ 97 %) lag innerhalb der Populationen, was intensiven Genfluss in der Vergangenheit widerspiegelt. Die genetische Differenzierung der Keimlinge war etwas erhöht (FST = 0.086) und ~ 91 % ihrer Variation lag innerhalb der Populationen. Im Gegensatz zu den adulten Bäumen konnte ich für Keimlinge ein „Isolation-by-distance“-Muster feststellen. Somit sind erste Hinweise auf begrenzten Genfluss im Keimlingsstadium infolge von Fragmentierung gegeben. Obwohl die Momentaufnahmen im Freiland keine Abnahme in der Frugivorenzahl und Samenausbreitung von P. africana als Folge von Fragmentierung beobachten ließen, weisen die Ergebnisse der genetischen Studie auf einen bereits reduzierten Genaustausch zwischen den Populationen hin. Somit lässt sich feststellen, dass die Faktoren Fragmentierung und Störung genetische Diversität, ökologische Prozesse und Artendiversität in Wäldern jeweils auf unterschiedliche Weise beeinflussen. Um Konsequenzen derartiger Einflüsse folgerichtig abschätzen zu können, sind Studien auf unterschiedlichen Diversitätsebenen unabdingbar.

Genetic dynamics across early life stages in the tropical tree Prunus africana (Rosaceae)

In many plant species, the genetic template of early life-stages is formed by animal-mediated pollination and seed dispersal and has profound impact on further recruitment and population dynamics. Understanding the impact of pollination and seed dispersal on genetic patterns is a central issue in plant population biology. In my thesis, I investigated (i) contemporary dispersal and gene flow distances as well as (ii) genetic diversity and spatial genetic structure (SGS) across subsequent recruitment stages in a population of the animal-pollinated and dispersed tree Prunus africana in Kakamega Forest, West Kenya. Using microsatellite markers and parentage analyses, I inferred distances of pollen dispersal (father-to-mother), seed dispersal/maternal gene flow (mother-to-offspring) as well as paternal gene flow (father-to-offspring) for four early life stages of the species (seeds and fruits, current year seedlings, seedlings ≤ 3yr, seedlings > 3yr). Distances of pollen and seed dispersal as well as paternal gene flow were significantly shorter than expected from the spatial arrangement of trees and sampling plots. They were not affected by the density of conspecific trees in the surrounding. At the propagule stage, mean pollen dispersal distances were considerably (23-fold) longer than seed dispersal distances, and paternal gene flow distances exceeded maternal gene flow by a factor of 25. Seed dispersal distances were remarkably restricted, potentially leading to a strong initial SGS. The initial genetic template created by pollination and seed dispersal was extensively altered during later recruitment stages. Potential Janzen-Connell effects led to markedly increasing distances between offspring and both parental trees in older life stages. This showed that distance and density-dependent mortality factors are not exclusively related to the mother tree, but also to the father. Across subsequent recruitment stages, the pollen to seed dispersal ratio and the paternal to maternal gene flow ratio dropped to 2.1 and 3.4, respectively, in seedlings > 3yr. The relative changes in effective pollen dispersal, seed dispersal, and paternal gene flow distances across recruitment stages elucidate the mechanisms affecting the contribution of the two processes pollen and seed dispersal to overall gene flow. Using the same six microsatellite loci, I analyzed genetic diversity and SGS across five life stages, from seed rain to adults. Levels of genetic diversity within the studied P. africana population were comparable to other Prunus species and did not vary across life stages. In congruence with the short seed dispersal distances, I found significant SGS in all life stages. SGS decreased from seed and early seedling stages to older juvenile stages, and it was higher in adults than in late juveniles of the next generation. A comparison of the data with direct assessments of contemporary gene flow patterns indicate that distance- or density-dependent mortality, potentially due to Janzen-Connell effects, led to the initial decrease in SGS. Intergeneration variation in SGS could have been driven by variation in demographic processes, the effect of overlapping generations, and local selection processes. Overall, my study showed that complex sequential processes during recruitment contribute to the spatial genetic structure of tree populations. It highlights the importance of a multistage perspective for a comprehensive understanding of the impact of animal-mediated pollen and seed dispersal on spatial population dynamics and genetic patterns of trees.