Gene and species trees of a Neotropical group of treefrogs: Genetic diversification in the Brazilian Atlantic Forest and the origin of a polyploid species

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

Atlantic forest fragmentation and genetic diversity of an isolated population of the Blue-manakin, Chiroxiphia caudata (Pipridae), assessed by microsatellite analyses

Habitat fragmentation is predicted to restrict gene flow, which can result in the loss of genetic variation and inbreeding depression. The Brazilian Atlantic forest has experienced extensive loss of habitats since European settlement five centuries ago, and many bird populations and species are vanishing. Genetic variability analysis in fragmented populations could be important in determining their long-term viability and for guiding management plans. Here we analyzed genetic diversity of a small understory bird, the Blue-manakins Chiroxiphia caudata (Pipridae), from an Atlantic forest fragment (112 ha) isolated 73 years ago, and from a 10,000 ha continuous forest tract (control), using orthologous microsatellite loci. Three of the nine loci tested were polymorphic. No statistically significant heterozygote loss was detected for the fragment population. Although genetic diversity, which was estimated by expected heterozygosity and allelic richness, has been lower in the fragment population in relation to the control, it was not statistically significant, suggesting that this 112 ha fragment can be sufficient to maintain a blue-manakin population large enough to avoid stochastic effects, such as inbreeding and/or genetic drift. Alternatively, it is possible that 73 years of isolation did not accumulate sufficient generations for these effects to be detected. However, some alleles have been likely lost, specially the rare ones, what is expected from genetic drift for such a small and isolated population. A high genetic differentiation was detected between populations by comparing both allelic and genotypic distributions. Only future studies in continuous areas are likely to answer if such a structure was caused by the isolation resulted from the forest fragmentation or by natural population structure.

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)

The genetic characterization of myrmelachista roger assemblages (hymenoptera: formicidae: formicinae) in the atlantic forest of southeastern Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Coeffcients of herdability and relatedness in a forest fragment of Araucaria angustifolia (Bertol.) Kuntze using genetic markers

Methods based on genetic markers to estimate the coefficient of heritability in natural populations are important to understand the effects of natural selection on inheritance of quantitative traits. The objective of this study was to investigate the genetic control of the trait plant height in a fragmented population of Araucaria angustifolia. This study was conducted in a forest fragment of 5.4 ha of area, located in the State of Parana, Brazil. Estimates of heritability were performed using data from genotypes and height of regenerating individuals of the population. Four methods to estimate the relatedness between pairs of individuals (RITLAND, 1996; LYNCH; RITLAND, 1999; QUELLER; GOODNIGHT, 1989; WANG, 2002) for three distances (without criteria, 25 and 50 m) were used. The coefficient of heritability estimated using the estimator of relatedness of Ritland (1996), suggest that the genetic control of the trait height is low in the regeneration, thus the natural selection as well as the artificial selection have a low potential to change the mean of the population. The estimates based on the other methods to calculate the relatedness presented low precision, indication that these methods are not adequate for the data used.

Botanical Preferences of Africanized Bees (Apis mellifera) on the Coast and in the Atlantic Forest of Sergipe, Brazil

Pollen analysis in honey can be used as an alternative method to research into flowers visited by bees in an area. This study aimed to indentify the main floral families in honey from apiaries in the Atlantic Forest and Sergipe state coast. Honey samples from these apiaries were studied, as well as plants that grow around them, which can be used as a source of foraging for bees. The palynological technique was used to compare the pollen content of honey samples with the pollen grains from leaves of plants found in the vicinity of the apiaries to assess whether they had been visited by bees. The results of studies in both sites were similar in terms of incompatibility of families found in the apiary vicinity and honey. Thus, it was possible to observe that in honey samples from the coast and in the remaining Atlantic forest, the number of families was greater than the number of families found in the apiary vicinity, which highlights the diversity of plants visited by bees and a possible expansion of the visited area for food search. This diversity suggests an adaptive foraging behavior to plant resources available in the environment, which may facilitate the pollination of these botanical families and consequently improve their genetic quality.

Habitat structure and food resources for wildlife across successional stages in a tropical forest

Tropical forests are experiencing an increase in the proportion of secondary forests as a result of the balance between the widespread harvesting of old-growth forests and the regeneration in abandoned areas. The impacts of such a process on biodiversity are poorly known and intensely debated. Recent reviews and multi-taxa studies indicate that species replacement in wildlife assemblages is a consistent pattern, sometimes stronger than changes in diversity, with a replacement from habitat generalists to old-growth specialists being commonly observed during tropical forest regeneration. However, the ecological drivers of such compositional changes are rarely investigated, despite its importance in assessing the conservation value of secondary forests, and to support and guide management techniques for restoration. By sampling 28 sites in a continuous Atlantic forest area in Southeastern Brazil, we assessed how important aspects of habitat structure and food resources for wildlife change across successional stages, and point out hypotheses on the implications of these changes for wildlife recovery. Old-growth areas presented a more complex structure at ground level (deeper leaf litter, and higher woody debris volume) and higher fruit availability from an understorey palm, whereas vegetation connectivity, ground-dwelling arthropod biomass, and total fruit availability were higher in earlier successional stages. From these results we hypothetize that generalist species adapted to fast population growth in resource-rich environments should proliferate and dominate earlier successional stages, while species with higher competitive ability in resource-limited environments, or those that depend on resources such as palm fruits, on higher complexity at the ground level, or on open space for flying, should dominate older-growth forests. Since the identification of the drivers of wildlife recovery is crucial for restoration strategies, it is important that future work test and further develop the proposed hypotheses. We also found structural and functional differences between old-growth forests and secondary forests with more than 80 years of regeneration, suggesting that restoration strategies may be crucial to recover structural and functional aspects expected to be important for wildlife in much altered ecosystems, such as the Brazilian Atlantic forest. (C) 2012 Elsevier B.V. All rights reserved.

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.

DEVELOPMENT AND APPLICATIONS OF GENOMIC RESOURCES FOR TWO NORTH AMERICAN HARDWOOD TAXA

Hardwoods comprise about half of the biomass of forestlands in North America and present many uses including economic, ecological and aesthetic functions. Forest trees rely on the genetic variation within tree populations to overcome the many biotic, abiotic, anthropogenic factors which are further worsened by climate change, that threaten their continued survival and functionality. To harness these inherent genetic variations of tree populations, informed knowledge of the genomic resources and techniques, which are currently lacking or very limited, are imperative for forest managers. The current study therefore aimed to develop genomic microsatellite markers for the leguminous tree species, honey locust, Gleditsia triacanthos L. and test their applicability in assessing genetic variation, estimation of gene flow patterns and identification of a full-sib mapping population. We also aimed to test the usefulness of already developed nuclear and gene-based microsatellite markers in delineation of species and taxonomic relationships between four of the taxonomically difficult Section Lobatae species (Quercus coccinea, Q. ellipsoidalis, Q. rubra and Q. velutina. We recorded 100% amplification of G. triacanthos genomic microsatellites developed using Illumina sequencing techniques in a panel of seven unrelated individuals with 14 of these showing high polymorphism and reproducibility. When characterized in 36 natural population samples, we recorded 20 alleles per locus with no indication for null alleles at 13 of the 14 microsatellites. This is the first report of genomic microsatellites for this species. Honey locust trees occur in fragmented populations of abandoned farmlands and pastures and is described as essentially dioecious. Pollen dispersal if the main source of gene flow within and between populations with the ability to offset the effects of random genetic drift. Factors known to influence gene include fragmentation and degree of isolation, which make the patterns gene flow in fragmented populations of honey locust a necessity for their sustainable management. In this follow-up study, we used a subset of nine of the 14 developed gSSRs to estimate gene flow and identify a full-sib mapping population in two isolated fragments of honey locust. Our analyses indicated that the majority of the seedlings (65-100% - at both strict and relaxed assignment thresholds) were sired by pollen from outside the two fragment populations. Only one selfing event was recorded confirming the functional dioeciousness of honey locust and that the seed parents are almost completely outcrossed. From the Butternut Valley, TN population, pollen donor genotypes were reconstructed and used in paternity assignment analyses to identify a relatively large full-sib family comprised of 149 individuals, proving the usefulness of isolated forest fragments in identification of full-sib families. In the Ames Plantation stand, contemporary pollen dispersal followed a fat-tailed exponential-power distribution, an indication of effective gene flow. Our estimate of δ was 4,282.28 m, suggesting that insect pollinators of honey locust disperse pollen over very long distances. The high proportion of pollen influx into our sampled population implies that our fragment population forms part of a large effectively reproducing population. The high tendency of oak species to hybridize while still maintaining their species identity make it difficult to resolve their taxonomic relationships. Oaks of the section Lobatae are famous in this regard and remain unresolved at both morphological and genetic markers. We applied 28 microsatellite markers including outlier loci with potential roles in reproductive isolation and adaptive divergence between species to natural populations of four known interfertile red oaks, Q. coccinea, Q. ellpsoidalis, Q. rubra and Q. velutina. To better resolve the taxonomic relationships in this difficult clade, we assigned individual samples to species, identified hybrids and introgressive forms and reconstructed phylogenetic relationships among the four species after exclusion of genetically intermediate individuals. Genetic assignment analyses identified four distinct species clusters, with Q. rubra most differentiated from the three other species, but also with a comparatively large number of misclassified individuals (7.14%), hybrids (7.14%) and introgressive forms (18.83%) between Q. ellipsoidalis and Q. velutina. After the exclusion of genetically intermediate individuals, Q. ellipsoidalis grouped as sister species to the largely parapatric Q. coccinea with high bootstrap support (91 %). Genetically intermediate forms in a mixed species stand were located proximate to both potential parental species, which supports recent hybridization of Q. velutina with both Q. ellipsoidalis and Q. rubra. Analyses of genome-wide patterns of interspecific differentiation can provide a better understanding of speciation processes and taxonomic relationships in this taxonomically difficult group of red oak species.

LiDAR remote sensing applied to forest resources assessment

Disponer de información precisa y actualizada de inventario forestal es una pieza clave para mejorar la gestión forestal sostenible y para proponer y evaluar políticas de conservación de bosques que permitan la reducción de emisiones de carbono debidas a la deforestación y degradación forestal (REDD). En este sentido, la tecnología LiDAR ha demostrado ser una herramienta perfecta para caracterizar y estimar de forma continua y en áreas extensas la estructura del bosque y las principales variables de inventario forestal. Variables como la biomasa, el número de pies, el volumen de madera, la altura dominante, el diámetro o la altura media son estimadas con una calidad comparable a los inventarios tradicionales de campo. La presente tesis se centra en analizar la aplicación de los denominados métodos de masa de inventario forestal con datos LIDAR bajo diferentes condiciones y características de masa forestal (bosque templados puros y mixtos) y utilizando diferentes bases de datos LiDAR (información proveniente de vuelo nacionales e información capturada de forma específica). Como consecuencia de lo anterior, se profundiza en la generación de inventarios forestales continuos con LiDAR en grandes áreas. Los métodos de masa se basan en la búsqueda de relaciones estadísticas entre variables predictoras derivadas de la nube de puntos LiDAR y las variables de inventario forestal medidas en campo con el objeto de generar una cartografía continua de inventario forestal. El rápido desarrollo de esta tecnología en los últimos años ha llevado a muchos países a implantar programas nacionales de captura de información LiDAR aerotransportada. Estos vuelos nacionales no están pensados ni diseñados para fines forestales por lo que es necesaria la evaluación de la validez de esta información LiDAR para la descripción de la estructura del bosque y la medición de variables forestales. Esta información podría suponer una drástica reducción de costes en la generación de información continua de alta resolución de inventario forestal. En el capítulo 2 se evalúa la estimación de variables forestales a partir de la información LiDAR capturada en el marco del Plan Nacional de Ortofotografía Aérea (PNOA-LiDAR) en España. Para ello se compara un vuelo específico diseñado para inventario forestal con la información de la misma zona capturada dentro del PNOA-LiDAR. El caso de estudio muestra cómo el ángulo de escaneo, la pendiente y orientación del terreno afectan de forma estadísticamente significativa, aunque con pequeñas diferencias, a la estimación de biomasa y variables de estructura forestal derivadas del LiDAR. La cobertura de copas resultó más afectada por estos factores que los percentiles de alturas. Considerando toda la zona de estudio, la estimación de la biomasa con ambas bases de datos no presentó diferencias estadísticamente significativas. Las simulaciones realizadas muestran que las diferencias medias en la estimación de biomasa entre un vuelo específico y el vuelo nacional podrán superar el 4% en áreas abruptas, con ángulos de escaneo altos y cuando la pendiente de la ladera no esté orientada hacia la línea de escaneo. En el capítulo 3 se desarrolla un estudio en masas mixtas y puras de pino silvestre y haya, con un enfoque multi-fuente empleando toda la información disponible (vuelos LiDAR nacionales de baja densidad de puntos, imágenes satelitales Landsat y parcelas permanentes del inventario forestal nacional español). Se concluye que este enfoque multi-fuente es adecuado para realizar inventarios forestales continuos de alta resolución en grandes superficies. Los errores obtenidos en la fase de ajuste y de validación de los modelos de área basimétrica y volumen son similares a los registrados por otros autores (usando un vuelo específico y parcelas de campo específicas). Se observan errores mayores en la variable número de pies que los encontrados en la literatura, que pueden ser explicados por la influencia de la metodología de parcelas de radio variable en esta variable. En los capítulos 4 y 5 se evalúan los métodos de masa para estimar biomasa y densidad de carbono en bosques tropicales. Para ello se trabaja con datos del Parque Nacional Volcán Poás (Costa Rica) en dos situaciones diferentes: i) se dispone de una cobertura completa LiDAR del área de estudio (capitulo 4) y ii) la cobertura LiDAR completa no es técnica o económicamente posible y se combina una cobertura incompleta de LiDAR con imágenes Landsat e información auxiliar para la estimación de biomasa y carbono (capitulo 5). En el capítulo 4 se valida un modelo LiDAR general de estimación de biomasa aérea en bosques tropicales y se compara con los resultados obtenidos con un modelo ajustado de forma específica para el área de estudio. Ambos modelos están basados en la variable altura media de copas (TCH por sus siglas en inglés) derivada del modelo digital LiDAR de altura de la vegetación. Los resultados en el área de estudio muestran que el modelo general es una alternativa fiable al ajuste de modelos específicos y que la biomasa aérea puede ser estimada en una nueva zona midiendo en campo únicamente la variable área basimétrica (BA). Para mejorar la aplicación de esta metodología es necesario definir en futuros trabajos procedimientos adecuados de medición de la variable área basimétrica en campo (localización, tamaño y forma de las parcelas de campo). La relación entre la altura media de copas del LiDAR y el área basimétrica (Coeficiente de Stock) obtenida en el área de estudio varía localmente. Por tanto es necesario contar con más información de campo para caracterizar la variabilidad del Coeficiente de Stock entre zonas de vida y si estrategias como la estratificación pueden reducir los errores en la estimación de biomasa y carbono en bosques tropicales. En el capítulo 5 se concluye que la combinación de una muestra sistemática de información LiDAR con una cobertura completa de imagen satelital de moderada resolución (e información auxiliar) es una alternativa efectiva para la realización de inventarios continuos en bosques tropicales. Esta metodología permite estimar altura de la vegetación, biomasa y carbono en grandes zonas donde la captura de una cobertura completa de LiDAR y la realización de un gran volumen de trabajo de campo es económica o/y técnicamente inviable. Las alternativas examinadas para la predicción de biomasa a partir de imágenes Landsat muestran una ligera disminución del coeficiente de determinación y un pequeño aumento del RMSE cuando la cobertura de LiDAR es reducida de forma considerable. Los resultados indican que la altura de la vegetación, la biomasa y la densidad de carbono pueden ser estimadas en bosques tropicales de forma adecuada usando coberturas de LIDAR bajas (entre el 5% y el 20% del área de estudio). ABSTRACT The availability of accurate and updated forest data is essential for improving sustainable forest management, promoting forest conservation policies and reducing carbon emissions from deforestation and forest degradation (REDD). In this sense, LiDAR technology proves to be a clear-cut tool for characterizing forest structure in large areas and assessing main forest-stand variables. Forest variables such as biomass, stem volume, basal area, mean diameter, mean height, dominant height, and stem number can be thus predicted with better or comparable quality than with costly traditional field inventories. In this thesis, it is analysed the potential of LiDAR technology for the estimation of plot-level forest variables under a range of conditions (conifer & broadleaf temperate forests and tropical forests) and different LiDAR capture characteristics (nationwide LiDAR information vs. specific forest LiDAR data). This study evaluates the application of LiDAR-based plot-level methods in large areas. These methods are based on statistical relationships between predictor variables (derived from airborne data) and field-measured variables to generate wall to wall forest inventories. The fast development of this technology in recent years has led to an increasing availability of national LiDAR datasets, usually developed for multiple purposes throughout an expanding number of countries and regions. The evaluation of the validity of nationwide LiDAR databases (not designed specifically for forest purposes) is needed and presents a great opportunity for substantially reducing the costs of forest inventories. In chapter 2, the suitability of Spanish nationwide LiDAR flight (PNOA) to estimate forest variables is analyzed and compared to a specifically forest designed LiDAR flight. This study case shows that scan angle, terrain slope and aspect significantly affect the assessment of most of the LiDAR-derived forest variables and biomass estimation. Especially, the estimation of canopy cover is more affected than height percentiles. Considering the entire study area, biomass estimations from both databases do not show significant differences. Simulations show that differences in biomass could be larger (more than 4%) only in particular situations, such as steep areas when the slopes are non-oriented towards the scan lines and the scan angles are larger than 15º. In chapter 3, a multi-source approach is developed, integrating available databases such as nationwide LiDAR flights, Landsat imagery and permanent field plots from SNFI, with good resultos in the generation of wall to wall forest inventories. Volume and basal area errors are similar to those obtained by other authors (using specific LiDAR flights and field plots) for the same species. Errors in the estimation of stem number are larger than literature values as a consequence of the great influence that variable-radius plots, as used in SNFI, have on this variable. In chapters 4 and 5 wall to wall plot-level methodologies to estimate aboveground biomass and carbon density in tropical forest are evaluated. The study area is located in the Poas Volcano National Park (Costa Rica) and two different situations are analyzed: i) available complete LiDAR coverage (chapter 4) and ii) a complete LiDAR coverage is not available and wall to wall estimation is carried out combining LiDAR, Landsat and ancillary data (chapter 5). In chapter 4, a general aboveground biomass plot-level LiDAR model for tropical forest (Asner & Mascaro, 2014) is validated and a specific model for the study area is fitted. Both LiDAR plot-level models are based on the top-of-canopy height (TCH) variable that is derived from the LiDAR digital canopy model. Results show that the pantropical plot-level LiDAR methodology is a reliable alternative to the development of specific models for tropical forests and thus, aboveground biomass in a new study area could be estimated by only measuring basal area (BA). Applying this methodology, the definition of precise BA field measurement procedures (e.g. location, size and shape of the field plots) is decisive to achieve reliable results in future studies. The relation between BA and TCH (Stocking Coefficient) obtained in our study area in Costa Rica varied locally. Therefore, more field work is needed for assessing Stocking Coefficient variations between different life zones and the influence of the stratification of the study areas in tropical forests on the reduction of uncertainty. In chapter 5, the combination of systematic LiDAR information sampling and full coverage Landsat imagery (and ancillary data) prove to be an effective alternative for forest inventories in tropical areas. This methodology allows estimating wall to wall vegetation height, biomass and carbon density in large areas where full LiDAR coverage and traditional field work are technically and/or economically unfeasible. Carbon density prediction using Landsat imaginery shows a slight decrease in the determination coefficient and an increase in RMSE when harshly decreasing LiDAR coverage area. Results indicate that feasible estimates of vegetation height, biomass and carbon density can be accomplished using low LiDAR coverage areas (between 5% and 20% of the total area) in tropical locations.

Conflicting laws and regulations : gridlock on the national forests : oversight hearing before the Subcommittee on Forests and Forest Health of the Committee on Resources, U.S. House of Representatives, One Hundred Seventh Congress, first session, December 4, 2001.

"Serial no. 107-76."

The forest resources of the Far Eastern Republic.

Mode of access: Internet.