Phenotypic plasticity and local adaptation favor range expansion of a Neotropical palm.

One of the most intriguing questions in plant ecology is which evolutionary strategy allows widely distributed species to increase their ecological range and grow in changing environmental conditions. Phenotypic plasticity and local adaptations are major processes governing species range margins, but little is known about their relative contribution for tree species distribution in tropical forest regions. We investigated the relative role of phenotypic plasticity and local adaptation in the ecological distribution of the widespread palm Euterpe edulis in the Brazilian Atlantic Forest. Genetic sampling and experiments were performed in old-growth remnants of two forest types with higher (Seasonal Semideciduous Forests vs. Submontane Rainforest) and lower biogeographic association and environmental similarities (Submontane Rainforest vs. Restinga Forest). We first assessed the molecular genetic differentiation among populations, focusing on the group of loci potentially under selection in each forest, using single-nucleotide polymorphism (SNPs) outliers. Further, we looked for potential adaptive divergence among populations in a common garden experiment and in reciprocal transplants for two plant development phases: seedling establishment and sapling growth. Analysis with outlier loci indicated that all individuals from the Semideciduous Forest formed a single group, while another group was formed by overlapping individuals from Submontane Rainforest and Restinga Forest. Molecular differentiation was corroborated by reciprocal transplants, which yielded strong evidence of local adaptations for seedling establishment in the biogeographically divergent Rainforest and Semideciduous Forest, but not for Restinga Forest and Submontane Rainforest. Phenotypic plasticity for palm seedling establishment favors range expansion to biogeographically related or recently colonized forest types, while persistence in the newly colonized ecosystem may be favored by local adaptations if climatic conditions diverge over time, reducing gene flow between populations. SNPs obtained by next-generation sequencing can help exploring adaptive genetic variation in tropical trees, which impose several challenges to the use of reciprocal transplants.

The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales.

The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora. In Brazil, the yellow passion fruit (Passiflora edulis) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of the P. edulis chloroplast genome, the first entirely sequenced in the Passifloraceae family. We determined its structure and organization, and also performed phylogenomic studies on the order Malpighiales and the Fabids clade. The P. edulis chloroplast genome is characterized by the presence of two copies of an inverted repeat sequence (IRA and IRB) of 26,154 bp, each separating a small single copy region of 13,378 bp and a large single copy (LSC) region of 85,720 bp. The annotation resulted in the identification of 105 unique genes, including 30 tRNAs, 4 rRNAs, and 71 protein coding genes. Also, 36 repetitive elements and 85 SSRs (microsatellites) were identified. The structure of the complete cp genome of P. edulis differs from that of other species because of rearrangement events detected by means of a comparison based on 22 members of the Malpighiales. The rearrangements were three inversions of 46,151, 3,765 and 1,631 bp, located in the LSC region. Phylogenomic analysis resulted in strongly supported trees, but this could also be a consequence of the limited taxonomic sampling used. Our results have provided a better understanding of the evolutionary relationships in the Malpighiales and the Fabids, confirming the potential of complete chloroplast genome sequences in inferring evolutionary relationships and the utility of long sequence reads for generating very accurate biological information.

Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populations

The study of the genetic structure of wild plant populations is essential for their management and conservation. Several DNA markers have been used in such studies, as well as isozyme markers. In order to provide a better comprehension of the results obtained and a comparison between markers which will help choose tools for future studies in natural populations of Oryza glumaepatula, a predominantly autogamous species, this study used both isozymes and microsatellites to assess the genetic diversity and genetic structure of 13 populations, pointing to similarities and divergences of each marker, and evaluating the relative importance of the results for studies of population genetics and conservation. A bulk sample for each population was obtained, by sampling two to three seeds of each plant, up to a set of 50 seeds. Amplified products of eight SSR loci were electrophoresed on non-denaturing polyacrylamide gels, and the fragments were visualized using silver staining procedure. Isozyme analyses were conducted in polyacrylamide gels, under a discontinuous system, using six enzymatic loci. SSR loci showed higher mean levels of genetic diversity (A=2.83, p=0.71, A P=3.17, Ho=0.081, He=0.351) than isozyme loci (A=1.20, p=0.20, A P=1.38, Ho=0.006, He=0.056). Interpopulation genetic differentiation detected by SSR loci (R ST=0.631, equivalent to F ST=0.533) was lower than that obtained with isozymes (F ST=0.772). However, both markers showed high deviation from Hardy-Weinberg expectations (F IS=0.744 and 0.899, respectively for SSR and isozymes). The mean apparent outcrossing rate for SSR ( =0.14) was higher than that obtained using isozymes ( =0.043), although both markers detected lower levels of outcrossing in Amazonia compared to the Pantanal. The migrant number estimation was also higher for SSR (Nm=0.219) than isozymes (Nm=0.074), although a small number for both markers was expected due to the mode of reproduction of this species, defined ...

El estudio de la estructura genética de poblaciones de plantas silvestres es esencial para su manejo y conservación. Varios marcadores de ADN e isoenzimas se han utilizado en este tipo de análisis. Con el fin de proporcionar una mejor comprensión de los resultados obtenidos y saber que marcador codominante elegir para futuros estudios en poblaciones naturales de Oryza glumaepatula, este trabajo busco evaluar y comparar dos marcadores de ADN, isoenzimas y microsatélites, en la diversidad y estructura genética de 13 poblaciones, destacando las similitudes y divergencias de cada marcador, así como la importancia relativa de los resultados en genética de poblaciones y conservación. Para los SSR, ocho loci SSR fueron evaluados, y los fragmentos se visualizaron utilizando el procedimiento de coloración con plata. Los análisis de isoenzimas se realizaron en geles de poliacrilamida, en los seis loci enzimáticos. Los loci SSR mostraron mayores niveles de diversidad genética que los loci isoenzimáticos, en promedio. La diferenciación genética entre los loci SSR (R ST=0.631, equivalente a F ST=0.533) fue inferior a la obtenida con las isoenzimas (F ST=0.772). Ambos marcadores mostraron alta desviación del equilibrio de Hardy-Weinberg (F IS=0.744 y 0.899, respectivamente, para SSR e isoenzimas). La tasa media aparente de cruzamiento para SSR ( =0.14) fue mayor que la obtenida con isoenzimas ( =0.043), aunque ambos marcadores detectaron niveles más bajos en la tasa de fecundación cruzada para la Amazonia, en comparación con la región del Pantanal. La estimación de número de migrantes también fue mayor para los SSR (Nm=0.219) que en isoenzimas (Nm=0.074). No se obtuvo ninguna correlación entre las distancias genéticas y geográficas para los SSR, y para las isoenzimas se obtuvo una correlación positiva entre las distancias genéticas y geográficas. Llegamos a la conclusión de que estos marcadores son divergentes en la detección de los parámetros de la diversidad genética en O. glumaepatula y que los microsatélites son más eficientes para detectar la información a nivel intra-poblacional, mientras que las isoenzimas son más potentes para detectar la diversidad entre poblaciones.

Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populations.

The study of the genetic structure of wild plant populations is essential for their management and conservation. Several DNA markers have been used in such studies, as well as isozyme markers. In order to provide a better comprehension of the results obtained and a comparison between markers which will help choose tools for future studies in natural populations of Oryza glumaepatula, a predominantly autogamous species, this study used both isozymes and microsatellites to assess the genetic diversity and genetic structure of 13 populations, pointing to similarities and divergences of each marker, and evaluating the relative importance of the results for studies of population genetics and conservation. A bulk sample for each population was obtained, by sampling two to three seeds of each plant, up to a set of 50 seeds. Amplified products of eight SSR loci were electrophoresed on non-denaturing polyacrylamide gels, and the fragments were visualized using silver staining procedure. Isozyme analyses were conducted in polyacrylamide gels, under a discontinuous system, using six enzymatic loci. SSR loci showed higher mean levels of genetic diversity (A=2.83, p=0.71, A(p)=3.17, H(o)=0.081, H(e)=0.351) than isozyme loci (A=1.20, p=0.20, A(p)=1.38, H(o)=0.006, H(e)=0.056). Interpopulation genetic differentiation detected by SSR loci (R(ST)=0.631, equivalent to F(ST)=0.533) was lower than that obtained with isozymes (F(ST)=0.772). However, both markers showed high deviation from Hardy-Weinberg expectations (F(IS)=0.744 and 0.899, respectively for SSR and isozymes). The mean apparent outcrossing rate for SSR (t(a)=0.14) was higher than that obtained using isozymes (t(a)=0.043), although both markers detected lower levels of outcrossing in Amazonia compared to the Pantanal. The migrant number estimation was also higher for SSR (Nm=0.219) than isozymes (Nm=0.074), although a small number for both markers was expected due to the mode of reproduction of this species, defined as mixed with predominance of self fertilization. No correlation was obtained between genetic and geographic distances with SSR, but a positive correlation was found between genetic and geographic distances with isozymes. We conclude that these markers are divergent in detecting genetic diversity parameters in O. glumaepatula and that microsatellites are powerful for detecting information at the intra-population level, while isozymes are more powerful for inter-population diversity, since clustering of populations agreed with the expectations based on the geographic distribution of the populations using this marker.

Genetic structure of Brazilian wild rice (Oryza glumaepatula Steud., Poaceae) populations analyzed using microsatellite markers

Knowledge of the genetic structure and diversity of natural populations is important in developing strategies for in situ and ex situ conservation. We used eight microsatellite loci to estimate genetic structure and investigate within and between population genetic variation in eleven Brazilian wild rice (Oryza glumaepatula) populations. The study showed the following genetic diversity parameters: average number of 3.1 alleles per locus; 77.3 percent polymorphic loci; 0.091 observed heterozygosity and 0.393 gene diversity. F-statistics detected by microsatellite loci were: F ST = 0.491 (and R ST = 0.608), F IS = 0.780 and F IT = 0.888. No population was in Hardy-Weinberg equilibrium. The estimated apparent outcrossing rate (0.143) indicated a predominance of self-fertilization. The gene flow values were low (Nm = 0.259 and 0.161 for F ST and R ST, respectively). Populations were spatially structured but without a correlation between genetic and geographic distances. Five populations (PG-4, PG-2, PU-1, SO-4, NE-18) were identified as priorities for conservation strategies. Populations from the Amazon biome showed heterogeneity with respect to intrapopulation diversity. The high level of genetic differentiation between populations and the high number of private alleles suggested that sampling should be carried out on a large number of O. glumaepatula populations for ex situ conservation purposes.

Mating system of Brazilian Oryza glumaepatula populations studied with microsatellite markers.

BACKGROUND AND AIMS: A knowledge of natural populations' breeding systems is important in order to implement in situ and ex situ management and conservation practices. Using microsatellite markers, three Oryza glumaepatula populations from Brazil were studied to determine the breeding system and genetic structure parameters of this species. METHODS: Each population represented by ten families with ten individuals per family was studied using eight microsatellite primers. Families of the Rio Xingu population (XI) were obtained from the greenhouse, whereas families from Rio Solimoes (SO) and Rio Paraguay (PG) were collected from the wild. Amplified products electrophoresed on non-denaturing polyacrylamide gels were visualized with a silver staining procedure. The mating system parameters were analysed based on the mixed mating model (software MLTR) while genetic structure analyses of the three populations and their families were performed using the FSTAT software. KEY RESULTS: The mean numbers of alleles per loci were 2.5, 3.9 and 2.5, respectively for the XI, PG and SO populations. Compared with their families, higher values for the observed heterozygosity and gene diversity were estimated for the parental populations. The subdivision (based on R(ST)) and inbreeding (F(IS)) in the SO and PG populations had similar effects, while inbreeding was the main effect in the families. Multilocus outcrossing rates varied from 0.011 to 0.223 in the three populations, indicating divergence in the outcrossing rates among O. glumaepatula populations. For the species (considering SO and PG populations together) an intermediate value was observed (tm = 0.116). Biparental inbreeding varied from 0.008 to 0.123, contributing to the selfing rate in these populations. More than 50 % of the outcrossing occurred between related individuals. CONCLUSIONS: The results indicated divergence in the mating system among O. glumaepatula populations, with consequences for conservation practices. The mating system of this species was classified as mixed with a predominance of self-fertilization.