SNP Markers as a Successful Molecular Tool for Assessing Species Identity and Geographic Origin of Trees in the Economically Important South American Legume Genus Dipteryx.

Dipteryx timber has been heavily exploited in South America since 2000s due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to 6 different Dipteryx species, was genotyped based on 171 molecular markers. After the exclusion of markers out of Hardy-Weinberg equilibrium or with no polymorphism or low amplification, 83 nuclear, 29 chloroplast, 13 mitochondrial single nucleotide polymorphisms (SNPs), and 2 chloroplast and 5 mitochondrial INDELS remained. Six genetic groups were identified using Bayesian Structure analyses of the nuclear SNPs, which corresponded to the different Dipteryx species collected in the field. Seventeen highly informative markers were identified as suitable for species identification and obtained self-assignment success rates to species level of 78-96%. An additional set of 15 molecular markers was selected to determine the different genetic clusters found in Dipteryx odorata and Dipteryx ferrea, obtaining self-assignment success rates of 91-100%. The success to assign samples to the correct country of origin using all or only the informative markers improved when using the nearest neighbor approach (69-92%) compared to the Bayesian approach (33-80%). While nuclear and chloroplast SNPs were more suitable for differentiating the different Dipteryx species, mitochondrial SNPs were ideal for determining the genetic clusters of D. odorata and D. ferrea. These 32 selected SNPs will be invaluable genetic tools for the accurate identification of species and country of origin of Dipteryx timber.

Correlation between genetic diversity and environmental suitability: taking uncertainty from ecological niche models into account.

The hindcast of shifts in the geographical ranges of species as estimated by ecological niche modelling (ENM) has been coupled with phylogeographical patterns, allowing the inference of past processes that drove population differentiation and genetic variability. However, more recently, some studies have suggested that maps of environmental suitability estimated by ENM may be correlated to species' abundance, raising the possibility of using environmental suitability to infer processes related to population demographic dynamics and genetic variability. In both cases, one of the main problems is that there is a wide variation in ENM development methods and climatic models. In this study, we analyse the relationship between heterozygosity (He) and environmental suitability from multiple ENMs for 25 population estimates for Dipteryx alata, a widely distributed, endemic tree species of the Cerrado region of central Brazil. We propose a new approach for generating a statistical distribution of correlations under randomly generated ENM. The confidence intervals from these distributions indicate how model selection with different properties affects the ability to detect a correlation of interest (e.g. the correlation between He and suitability). Additionally, our approach allows us to explore which particular ensemble of ENMs produces the better result for finding an association between environmental suitability and He. Caution is necessary when choosing a method or a climatic data set for modelling geographical distributions, but the new approach proposed here provides a conservative way to evaluate the ability of ensembles to detect patterns of interest.

Geographic shifts in climatically suitable areas and loss of genetic variability in Dipteryx alata ("Baru" Tree; Fabaceae).

Many species are expected to suffer strong shifts in their geographic ranges due to climate changes in the next 50 years, with severe consequences for biodiversity patterns and population structure. We used here an ensemble forecast approach for obtaining species' range in which multiple species distribution models and climatic models were combined to model loss of genetic variability in Baru, Dipteryx alata (Fabaceae), an economically important Neotropical tree native to the Cerrado of Brazil. We estimated a series of genetic parameters (number of alleles per locus, expected heterozygosity under Hardy-Weinberg equilibrium and mutation-drift equilibrium) for this species based on eight microsatellite loci. We then recalculated these parameters assuming that local populations in areas of low future environmental suitability will go extinct. All genetic parameters remained approximately constant up to a 50% threshold of climatic suitability in the future; after this critical threshold there is an abrupt reduction in all parameters, although the magnitude of shift is only about 10% of current values, on average. Thus, despite the shifts in geographic range and climatically suitable areas towards southeastern Brazil, our analyses do not predict a strong loss of genetic diversity in D. alata because of the broad tolerance of this species, which ensures large future ranges, contrasting with other Cerrado species that have been analyzed in a similar manner.

Combining multiple models to predict the geographical distribution of the Baru tree (Dipteryx alata Vogel) in the Brazilian Cerrado.

The Brazilian Cerrado is a biome of great biodiversity, but detailed information about the diversity and distribution of species in this region is still insufficient for both testing ecological hypotheses and for conservation purposes. Among native plants in the Cerrado, Dipteryx alata Vogel (commonly known as the "Baru" tree), has a high potential for exploitation. The aims of this paper were to predict the potential spatial distribution of D. alata in the Brazilian Cerrado utilising five different niche modelling techniques. These techniques usually provide distinct results, so it may be difficult to choose amongst them. To adjust for this uncertainty, we employ an ensemble forecasting approach to predict the spatial distribution of the Baru tree. We accumulated a total of 448 occurrence points and modelled the subsequent predicted occurrences using seven climatic variables. Five different presence-only ecological niche modelling techniques (GARP, Maxent, BIOCLIM, Mahalanobis Distance and Euclidean Distance) were used and the performance of these models was compared using Receiver Operating Characteristics (ROC) and the Area Under the Curve (AUC). All models presented AUC values higher than 0.68, and GARP presented the highest AUC value, whereas Euclidean Distance presented the lowest. The ensemble forecasting approach suggested a high suitability for the occurrence of the Baru tree in the Central-Western region of the Brazilian Cerrado. Our study demonstrated that modelling species distribution using ensemble forecasting can be an important computational tool for better establishing sampling strategies and for improving our biodiversity knowledge to better identify priority areas for conservation. For the Baru tree, we recommend priority actions for conservation in the central region of the Cerrado Biome.

Ecological consequences of primary and secondary seed dispersal on seed and seedling fate of Dipteryx oleifera (Fabaceae)

The relative contributions of primary and secondary seed dispersal to plant demography have received little investigation. Evidence on these seed dispersal types, on seed fate and seedling recruitment of the tropical rain forest tree Dipteryx oleifera, is presented. The study was conducted in a 6.37ha permanent plot where seeds and seedlings were located and tagged for the 2007 cohort. A total of 2 814 seeds were threaded and their fate was followed one year after germination. Primary seed dispersal by bats protected seeds from insect larval predation below the adult tree. Bats congregated seeds in bat seed piles located at a mean distance of 40.94±1.48m from the nearest adult individual of D. oleifera. Terrestrial vertebrates congregated seeds in caches located 41.90±2.43m from the nearest adult individual of D. oleifera. The results of the fitted proportional hazard model suggested that primary seed dispersal decreased seed hazard probability by 1.12% for each meter from the adult conspecific (p<0.001) and that secondary seed dispersal decreased it by 23.97% (p<0.001). Besides, the odds ratio regression models results showed that the overall effect of unviable seeds was a reduction in viable seed predation rate. For each unviable seed deposited by bats into the seed piles, the rate of seed predation by terrestrial vertebrates decreased 6% (p<0.001). For each damaged seed by terrestrial vertebrates in the seed piles, the rate of germination decreased 4% (p<0.001). For each germinated seed in the seed piles, the rate of recruitment increased 16% (p=0.001). Seedling survival of seeds that emerged after secondary seed dispersal events, showed no statistically significant difference in arthropod herbivory, in relation to seedlings that came from seeds that were dispersed only primarily by bats (F=0.153, p=0.697, df=1.98). Thus both primary and secondary dispersal contributed to higher seedling survival away from the nearest adult D. oleifera (r2=0.713, n=578, p=0.004). The distribution of D. oleifera seedlings is consistent with the Janzen-Connell Hypothesis and depends on primary dispersal by bats, secondary dispersal by terrestrial vertebrates, a seed masking effect and, the constant threat of insect herbivores on seedlings. Rev. Biol. Trop. 58 (3): 991-1007. Epub 2010 September 01.

Presentamos evidencia de la contribución relativa de la dispersión primaria y secundaria de semillas en la suerte que corren las mismas y en el reclutamiento de plántulas de la especie de bosque húmedo tropical Dipteryx oleifera. Este estudio fue realizado en una parcela permanente de 6.37 ha en la que semillas y plántulas del cohorte del 2007 fueron localizadas y mapeadas. Etiquetamos 2 814 semillas para evaluar su suerte un año después de la germinación. Encontramos que la dispersión primaria por murciélagos libera a las semillas de la depredación bajo la copa del árbol adulto causada por la fase larval de un insecto. Los murciélagos dispersan semillas bajo la copa de palmas usadas como comederos, localizados a 40.94±1.48m del árbol de D. oleifera más cercano y vertebrados terrestres congregaran las semillas en caches localizados aproximadamente a 41.90±2.43m del árbol de D. oleifera. Un modelo proporcional de riesgos fue ajustado a los datos de semillas y los resultados sugieren que la dispersión decrece la probabilidad de mortalidad de las semillas 1.16% por cada metro del árbol conspecífico más cercano (p<0.001) y la dispersión secundaria de semillas decrece la probabilidad de mortalidad 23.94% por cada metro (p<0.001). Los modelos de regresión de quebrados muestran que las semillas inviables reducen la tasa de depredación de las viables. Por cada semilla inviable depositada por los murciélagos en las agrupaciones de semillas, la tasa de depredación por vertebrados terrestres decreció 6% (p<0.001). Por cada semilla dañada por vertebrados en las agrupaciones, la tasa de germinación decreció 4% (p<0.001). Por cada semilla germinada en las agrupaciones, la tasa de reclutamiento incrementó 16% (p=0.000). La sobrevivencia de plántulas con dispersión secundaria fue estadísticamente diferente a la de aquellas que únicamente tuvieron dispersión primaria (F=0.153, p=0.697, df=1.98). Ambos tipos de dispersión contribuyeron con una alta sobrevivencia de plántulas lejos del árbol congénere más cercano (r²=0.713, n=578, p=0.004). Concluimos que la distribución de las plántulas de D. oleifera es consistente con la Hipótesis de Janzen- Connell y depende de la dispersión primaria por murciélagos, dispersión secundaria por vertebrados terrestres, el efecto de enmascaramiento y el constante ataque de insectos herbívoros a las plántulas.

Ecological consequences of primary and secondary seed dispersal on seed and seedling fate of Dipteryx oleifera (Fabaceae).

The relative contributions of primary and secondary seed dispersal to plant demography have received little investigation. Evidence on these seed dispersal types, on seed fate and seedling recruitment of the tropical rain forest tree Dipteryx oleifera, is presented. The study was conducted in a 6.37ha permanent plot where seeds and seedlings were located and tagged for the 2007 cohort. A total of 2 814 seeds were threaded and their fate was followed one year after germination. Primary seed dispersal by bats protected seeds from insect larval predation below the adult tree. Bats congregated seeds in bat seed piles located at a mean distance of 40.94 +/- 1.48m from the nearest adult individual of D. oleifera. Terrestrial vertebrates congregated seeds in caches located 41.90 +/- 2.43m from the nearest adult individual of D. oleifera. The results of the fitted proportional hazard model suggested that primary seed dispersal decreased seed hazard probability by 1.12% for each meter from the adult conspecific (p<0.001) and that secondary seed dispersal decreased it by 23.97% (p<0.001). Besides, the odds ratio regression models results showed that the overall effect of unviable seeds was a reduction in viable seed predation rate. For each unviable seed deposited by bats into the seed piles, the rate of seed predation by terrestrial vertebrates decreased 6% (p<0.001). For each damaged seed by terrestrial vertebrates in the seed piles, the rate of germination decreased 4% (p<0.001). For each germinated seed in the seed piles, the rate of recruitment increased 16% (p=0.001). Seedling survival of seeds that emerged after secondary seed dispersal events, showed no statistically significant difference in arthropod herbivory, in relation to seedlings that came from seeds that were dispersed only primarily by bats (F=0.153, p=0.697, df=1.98). Thus both primary and secondary dispersal contributed to higher seedling survival away from the nearest adult D. oleifera (r2=0.713, n=578, p=0.004). The distribution of D. oleifera seedlings is consistent with the Janzen-Connell Hypothesis and depends on primary dispersal by bats, secondary dispersal by terrestrial vertebrates, a seed masking effect and, the constant threat of insect herbivores on seedlings.

Recruitment dynamics of the tropical rainforest tree Dipteryx oleifera (Fabaceae) in eastern Nicaragua.

Seed production, seed dispersal and recruitment are critical processes in population dynamics, because they are almost never completely successful. We recorded the recruitment dynamics for the population of Dipteryx oleifera in a tropical rainforest in eastern Nicaragua (12 degrees 05' N., 83 degrees 55' W.) from March 2002 to August 2006. Seeds and seedlings had highly clumped distributions, while sapling distributions appeared to be random. Seedling survival increased away from the nearest conspecifc adult tree, where seedling density is lower. Since relative growth rates of seedlings are not correlated with the distance to the nearest conspecific adult, seedling survival appears to be independent of seedling growth. Seedling density is inversely correlated with seedling insect herbivory damage. Seedling survival correlated negatively with the number of saplings per sub-plot (10x10 m), suggesting that insect herbivore may also cue in on saplings rather than only on adult D. oleifera trees in order to locate seedlings. Seedling establishment is significantly clumped with respect to the nearest adult tree. Larger clumps of seedlings seems more ephemeral than isolated smaller clumps located away from the nearest D. oleifera tree. These results support current empirical evidence presented earlier for the Janzen-Connell hypothesis for Dipteryx oleifera at seed and seedling stages and, the Recruitment Limitation hypothesis at the sapling stage, because sapling individuals might have recruited after random light-gap formation.

Recruitment dynamics of the tropical rainforest tree Dipteryx oleifera (Fabaceae) in eastern Nicaragua

Seed production, seed dispersal and recruitment are critical processes in population dynamics, because they are almost never completely successful. We recorded the recruitment dynamics for the population of Dipteryx oleifera in a tropical rainforest in eastern Nicaragua (12°05’ N., 83°55’ W.) from March 2002 to August 2006. Seeds and seedlings had highly clumped distributions, while sapling distributions appeared to be random. Seedling survival increased away from the nearest conspecifc adult tree, where seedling density is lower. Since relative growth rates of seedlings are not correlated with the distance to the nearest conspecific adult, seedling survival appears to be independent of seedling growth. Seedling density is inversely correlated with seedling insect herbivory damage. Seedling survival correlated negatively with the number of saplings per sub-plot (10x10m), suggesting that insect herbivore may also cue in on saplings rather than only on adult D. oleifera trees in order to locate seedlings. Seedling establishment is significantly clumped with respect to the nearest adult tree. Larger clumps of seedlings seems more ephemeral than isolated smaller clumps located away from the nearest D. oleifera tree. These results support current empirical evidence presented earlier for the Janzen-Connell hypothesis for Dipteryx oleifera at seed and seedling stages and, the Recruitment Limitation hypothesis at the sapling stage, because sapling individuals might have recruited after random light-gap formation. Rev. Biol. Trop. 57 (1-2): 321-338. Epub 2009 June 30.

Resumen Estudiamos la dinámica de regeneración de la población de Dipteryx oleifera en un bosque húmedo tropical del este de Nicaragua. Semillas y plántulas se encuentran altamente agregadas, pero la distribución de vástagos podría ser al azar. La supervivencia de plántulas aumenta con la distancia al congéner más cercano, donde la densidad de plántulas es más baja. Como las tasas de crecimiento relativo de plántulas no se correlacionan con la distancia al congénere más cercano, la supervivencia de las plantas pareciera no estar determinada por el crecimiento de plántulas. La densidad de plántulas está inversamente correlacionada con los niveles de daño de herbivoría insectívora. La supervivencia de plántulas se correlaciona negativamente con el número de vástagos, lo cuál sugiere que los insectos herbívoros podrían estar localizando vástagos y árboles y de allí, las plántulas. La supervivencia de plántulas presentó una distribución significativamente agrupada lejos de los congéneres más cercanos. Los parches de plántulas más grandes fueron más efímeros que los parches pequeños y aislados ubicados lejos de los árboles adultos. Los resultados coinciden con la hipótesis de Janzen-Connell sobre estados de semilla y plántula. Además, ofrecen evidencia en favor de la hipótesis de Limitación de Reclutamiento para los vástagos, ya que los vástagos podrían estar estableciéndose en claros de luz pequeños que se forman al azar.

Landscape conservation genetics of Dipteryx alata ("baru" tree: Fabaceae) from Cerrado region of central Brazil.

In this paper random amplified polymorphic DNA (RAPD) was used to evaluate the degree of among-population differentiation and associated spatial patterns of genetic divergence for Dipteryx alata Vogel populations from Cerrado region of central Brazil, furnishing support for future programs of conservation of this species. We analyzed patterns of genetic and spatial population structure using 45 RAPD loci scored for 309 trees, sampled from five different regions with two populations each. Genetic structure analysis suggested that panmixia null hypothesis can be rejected, with significant among-population components of 15%. Hierarchical partition by Analysis of Molecular Variance (AMOVA) shows that 5% of genetic variation is within regions, whereas 10% of variation is among regions, and these results were confirmed by a Bayesian analyses on HICKORY. The Mantel correlogram revealed that this divergence is spatially structured, so that local populations situated at short geographic distances could not be considered independent units for conservation and management. However, genetic discontinuities among populations were found in the northwest and southeast parts of the study area, corresponding to regions of recent socio-economic expansion and high population density, respectively. Taking both geographic distances and genetic discontinuities into account it is possible to establish a group of population to be conserved, covering most of D. alata geographic distribution and congruent with previously established priority areas for conservation in the Cerrado region.