High levels of genetic divergence and inbreeding in populations of cupuassu (Theobroma grandiflorum) (original) (raw)
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Heredity, 2011
Understanding the mating patterns of populations of tree species is a key component of ex situ genetic conservation. In this study, we analysed the genetic diversity, spatial genetic structure (SGS) and mating system at the hierarchical levels of fruits and individuals as well as pollen dispersal patterns in a continuous population of Theobroma cacao in Pará State, Brazil. A total of 156 individuals in a 0.56 ha plot were mapped and genotyped for nine microsatellite loci. For the mating system analyses, 50 seeds were collected from nine seed trees by sampling five fruits per tree (10 seeds per fruit). Among the 156 individuals, 127 had unique multilocus genotypes, and the remaining were clones. The population was spatially aggregated; it demonstrated a significant SGS up to 15 m that could be attributed primarily to the presence of clones. However, the short seed dispersal distance also contributed to this pattern. Population matings occurred mainly via outcrossing, but selfing was observed in some seed trees, which indicated the presence of individual variation for self-incompatibility. The matings were also correlated, especially within (r p(m) ¼ 0.607) rather than among the fruits (r p(m) ¼ 0.099), which suggested that a small number of pollen donors fertilised each fruit. The paternity analysis suggested a high proportion of pollen migration (61.3%), although within the plot, most of the pollen dispersal encompassed short distances (28 m). The determination of these novel parameters provides the fundamental information required to establish long-term ex situ conservation strategies for this important tropical species.
Revista de Biología Tropical, 2016
The quantification of genetic diversity and intrapopulation spatial genetic structure (SGS) of tree species are important aspects for in and ex situ conservation practices. In this study we seek to understand the importance of conservation areas by quantifying the genetic diversity and the spatial genetic structure of a natural population of Theobroma speciosum. Within this population, 49 adults and 51 subadults were genotyped for five microsatellite loci. The results showed that adults and subadults have similar levels of genetic diversity and inbreeding (adults: A= 10.4, Ae = 10.3, F= 0.68, subadults: A= 10.6, Ae= 10.6, F= 0.57). Genetic diversity was spatially structured within the population, and the results suggest that near-neighbor trees up to a distance of 70 m are likely related. SGS is likely the result of short-distance seed dispersal, the short-distance range of pollinators, and infrequent breaches of the self-incompatible mating system. Considering the high demographic ...
Monitoring genetic diversity in tropical trees with multilocus dominant markers
Heredity, 2005
Since no universal codominant markers are currently available, dominant genetic markers, such as amplified fragment length polymorphism (AFLP), are valuable tools for assessing genetic diversity in tropical trees. However, the measurement of genetic diversity (H) with dominant markers depends on the frequency of null homozygotes (Q) and the fixation index (F) of populations. While Q can be estimated for AFLP loci, F is less accessible. Through a modelling approach, we show that the monolocus estimation of genetic diversity is strongly dependent on the value of F, but that the multilocus diversity estimate is surprisingly robust to variations in F. The robustness of the estimate is due to a mechanistic effect of compensation between negative and positive biases of H by different AFLP loci exhibiting contrasting frequency profiles of Q. The robustness was tested across contrasting theoretical frequency profiles of Q and verified for 10 neotropical species. Practical recommendations for the implementation of this analytical method are given for genetic surveys in tropical trees, where such markers are widely applied. Heredity (2005) 95, 274-280.
Conservation Genetics, 2006
A sample of 94 accessions of Theobroma cacao L. (cacao), representing four populations from the Brazilian Amazon (Acre, Rondoˆnia, lower Amazon and upper Amazon) were analyzed using microsatellite markers to assess the genetic diversity and the natural population structure. From the 19 microsatellite loci tested, 11 amplified scorable products, revealing a total of 49 alleles, including two monomorphic loci. The Brazilian upper Amazon population contained the largest genetic diversity, with the most polymorphic loci, the highest observed heterozygosity; and the majority of rare alleles, thereby this region might be considered part of the center of diversity of the species. The observed heterozygosity for all the Brazilian populations (H o =0.347) was comparable with values reported for other similar upper Amazon Forastero cacao populations, with the Acre and Rondoˆnia displaying the lowest values. The lower Amazon population, traditionally defined as highly homozygous, presented an unexpectedly high observed heterozygosity (H o =0.372), disclosing rare and distinct alleles, with large identity with the upper Amazon population. It was hypothesized that part of the lower Amazon population might derive from successive natural or intentional introduction of planting material from other provenances, mainly upper Amazon. Most of the loci exhibited a lower observed heterozygosity than expected, suggesting that self-pollination might be more common than usually assumed in cacao, but excess of homozygotes might also derive from sub-grouping (Wahlund effect) or from sampling related individuals. Most of the gene diversity was found to occur within groups, with small differentiation between the four Brazilian Amazon populations, typical of species with high gene flow.
Genetic diversity within and among populations of a
Erodium paularense Fern. Gonz. & Izco (Geraniaceae) is a perennial, endemic species of central Spain. The restricted distribution of its three populations has made it necessary to consider measures for conservation. Random amplified polymorphic DNA markers were used to determine genetic variation among and within populations. Sixty-three per cent of the bands were polymorphic. No population-specific marker was identified. Cluster analysis based on Jaccard's coefficient of all the individuals grouped most of them according to the present populations. Within-population variability was of a similar order in the three populations. Highly significant genetic differences between populations were detected through A M O V A. Within population diversity contributed 80435% to the species diversity, a value typical of an outbreeding plant.
Anadenanthera colubrina var cebil is a tree species native to the Upper Parana Atlantic Forest where human activities have severely impacted causing deep fragmentation. Microsatellites are not available in this species. Therefore, the first objective of this study was to generate chloroplast simple sequence repeats (cpSSR) by cross-species transfer. Understanding the evolutionary dynamics of subdivided populations is an important matter. In this way, a first approach to the characterization of the haplotypic diversity within and between populations as well as the genetic structure of native Argentinean populations were the main goals of this study. Twenty four individuals from two populations of the Misiones province were studied and four cpSSR loci were tested. Two of them exhibited polymorphic patterns leading to the identification of 11 cpDNA haplotypes with high mean genetic diversity (GD = 0.73). The minimum spanning network defined three clear groups which can be assigned to at least three subpopulations. AMOVA indicated that the total variance showed the highest percentage of variation (48 %) within subpopulations with a fixation index (F ST) statistically significant (F ST = 0.520; p < 0.05). Brown's two loci component analysis indicated that substructure population is present. Jost's differentiation global index (D est) was 0.049 while D est pairwise comparison reflected a certain level of genetic structure. The high diversity level detected in the adult trees of A. colubrina var cebil from the populations under study could be due to recent human influence. In this way, the reduction in population size caused a reduction in the number of trees leading to surviving trees showing the historical diversity of the populations analyzed.
Genetic diversity in natural populations of Theobroma subincanum Mart. in the Brazilian Amazon
Genetics and Molecular Research, 2013
Genetic diversity in Theobroma subincana Mart. molecular variance revealed that the variability between populations (51.71%) was higher than that within populations (48.29%). Among the three populations, CPT showed the highest diversity index and percentage of polymorphism. The ISSR molecular markers were efficient and presented sufficient polymorphism to estimate genetic diversity in populations of T. subincanum Mart.
2012
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 (H 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 (q p = 0.081). The inbreeding values within (f =-0.555) and among populations (F =-0.428) were low showing lacking of endogamy and a surplus of heterozygotes. The estimated gene flow (N 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. Index terms: Conservation, gene flow, genetic resources, genetic variability, isozyme, mangabeira. DIVERSIDADE E ESTRUTURA GENÉTICA EM POPULAÇÕES NATURAIS DE Hancornia speciosa var. speciosa GOMES NO NORDESTE DO BRASIL RESUMO-Hancornia speciosa Gomes é uma árvore frutífera nativa do Brasil, pertencente à família Apocinaceae, e é conhecida popularmente como Mangabeira. Seus frutos são amplamente consumidos in natura ou processados como sucos, sorvetes e geleias. O extrativismo e a intensa atividade antrópica no ambiente de ocorrência natural da Mangabeira, no Nordeste do Brasil, têm causado erosão genética na espécie e pouco se conhece sobre a estrutura genética das populações desta espécie. O objetivo deste trabalho foi avaliar a diversidade e a estrutura genética de populações naturais de H. speciosa var. speciosa. Utilizando 11 locos isoenzimáticos, avaliaram-se 164 indivíduos, amostrados em seis populações naturais localizadas nos Estados de Pernambuco e Alagoas, Nordeste do Brasil. Os resultados mostraram um alto nível de diversidade genética dentro da espécie (H e = 0,36), sendo verificado que a maior parte da variabilidade genética se encontra dentro das populações, com pequena diferenciação entre as mesmas (q p = 0,081). A endogamia dentro das populações (f =-0,555) e entre elas (F =-0,428) foi baixa, evidenciando ausência de endogamia e excesso de heterozigotos. O fluxo gênico estimado (N m) foi elevado, variando de 2,20 a 13,18, valores considerados suficientes para evitar os efeitos da deriva genética e a diferenciação genética entre as populações. As análises multivariadas indicam que há relação entre distância genética e espaço geográfico, hipótese esta que foi confirmada por uma análise de padrão espacial,utilizando o teste de Mantel (r = 0,3598; p = 0,0920) com 1.000 permutações aleatórias. O alto índice de diversidade genética nas populações indica potencial para a conservação genética in situ. Termos para indexação: Conservação de recursos genéticos, fluxo gênico, variabilidade genética, isoenzimas, Mangabeira.^^^^
Forest Ecology and Management, 2020
The aims of this study were to investigate the intrapopulation spatial genetic structure (SGS) of a preserved Swietenia macrophylla population in a managed forest in Southwestern Amazon, in Acre state, Brazil, and assess the genetic parameters that underlie the conceptual framework that guides conservation and management strategies. The study was conducted in Annual Production Unit (APU) 3, where 83 adult trees (DBH ≥ 40 cm) were mapped (1650 ha). The diameter at breast height (DBH) was measured and the vascular exchange was sampled. Leaf tissues were collected from 187 juvenile individuals within a radius of 20 m of adults. The population presented high heterozygosity (H o) for adult (0.767) and juvenile (0.763) individuals, but significantly high allelic richness (R) and significantly lower fixation index (F) in adults (R = 10.3, F = 0.048) than juveniles (R = 9.3, F = 0.119). The F value significantly higher for juveniles, suggesting selection against inbred individuals between juvenile and adult life stages. SGS was detected for adults up to 300 m. Mating was mainly through outcrossing (0.97-1.0), but some crossing occurred among related trees (0.02-0.16) and were correlated (r pm = 0.06-0.22), indicating a mean effective number of pollen donors ranging from 4.5 to 18.2. Pollen dispersal distances reached 3905 m (mean of 1472 m), and mean effective pollination neighbor area of 792 ha. The effective population size (N e) within family (2.73) was lower than expected for random mating populations. The number of trees (m) required for seed collection was estimated at 55 non-inbreed and not related trees to each other. The core collection consisted of 42 (50.6%) adults across the area. These individuals should be included in seed collection as they represent 100% of the total detected genetic diversity. The inclusion of S. macrophylla on the list of species available for exploitation is not indicated, because the species requires cross breeding for its maintenance and logging reduce the N e and may negatively impact the pattern of genetic diversity. These will significantly increase the risk of genetic erosion and population extinction due to a lack of adaptive ability. Adults serve as pollen donors that ecologically and genetically contribute to the maintenance of gene flow and N e. Because it is recognized as a threatened species worldwide, and due to the fact that in areas of natural occurrence the species presents low-density and shows difficulty establishing natural regeneration, we recommend that S. macrophylla be protected from selective logging.