Genetic diversity of Anadenanthera colubrina Vell.(Brenan) var cebil, a tree species from the South American subtropical forest as revealed by cpSSR markers (original) (raw)
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Journal of Forest Research, 2017
Anadenanthera colubrina (Vell.) Brenan var. cebil (Griseb.) Altschul is a tree species in South America important for its cultural, economic, and medicinal uses. In addition, it represents a trace in memory of the forests that have decreased over the years and for this reason it is not only interesting to study but also important to preserve the tree species for future generations. In this paper, we have characterized the genetic diversity of four populations. We collected seeds from four different sites: San Bernardo (B), El Cebilar (C), Metán (M), and El Gallinato (G) in Salta Province, North Argentina. We then compared the intergenic transcribed sequences of ribosomal DNA, a known genetic molecular marker. Our previous results, obtained through the morphological and genetic analysis of only four individuals (one for each zone), have showed that the individuals from B and M sites were more similar to each other as well as the individuals from G and C sites. In this paper, a larger number of individuals (25) were characterized and their phylogenetic relationships were computed. The results confirmed the previously found similarities.
Genetic Resources and Crop Evolution, 2007
Genetic diversity within and among 12 populations of the dioecious tropical tree species Hagenia abyssinica (Bruce) J.F. Gmel. in Ethiopia was examined with eight inter simple sequence repeat (ISSR) primers. A total of 104 clearly scorable bands were generated, among which 84 (81%) were polymorphic. Jaccard similarity coefficient was calculated for pairwise comparisons among all 120 individuals and ranged from 0.30 to 0.88 while average within-population similarity ranged from 0.53 to 0.66. Within-population variability was estimated as percentage polymorphic loci (ranging from 52% to 87%), Shannon’s information index (0.30–0.50) and Nei’s genetic diversity (0.21–0.35). The highest variability values were obtained for one recently planted population and for one wild population growing in an undisturbed primary forest area. Significant overall differentiation among populations was detected by both Shannon’s information index (0.26) and G ST (0.25). Relatedness among samples was estimated with a principal coordinate analysis, and relatedness among populations was estimated with a cluster analysis (UPGMA). A Mantel test indicated a significant association between genetic and geographic distances, and an autocorrelation analysis showed significant evidence of gene flow over distances up to 30 km. This study is the first of its kind for H. abyssinica, which has decreased recently in Ethiopia and now must be regarded as an endangered species. Both within-population and between-population diversity estimates are typical of outcrossing, longlived and late successional species, suggesting that recent anthropogenic disturbances have not yet had much impact on population genetic parameters. DNA marker data can, however, be used to identify the most suitable sites for in situ conservation and for collection of material for establishment of genebanks and plant improvement programs.
Review Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers
2014
Molecular markers have proven to be invaluable tools for assessing plants' genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra-and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.
Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers
Diversity, 2014
Molecular markers have proven to be invaluable tools for assessing plants' genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra-and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.
Biodiversity and Conservation, 2005
We have investigated levels of genetic diversity within and among seven remnant populations of Caesalpinia echinata Lam., an endangered species found as fragmented populations in three major areas around the coastal regions of Brazil. Using amplified fragment length polymorphism (AFLP) genetic markers, we detected levels of within-population genetic diversity ranging from 0.092 to 0.163, with the lowest values generally being found in the smallest populations. Estimates of between-population genetic differentiation were strongly correlated with geographical distance (r = 0.884, p < 0.001), which,along with a neighbour-joining phylogenetic analysis, strongly suggested high levels of genetic isolation by distance. Over half (62%) of the total genetic diversity was partitioned between populations, further highlighting the genetic distinctness of individual populations. Taken together, these results suggest that fragmentation has led to an increase in population differentiation betwe...
Genetics
In Mesoamerica, tropical dry forest is a highly threatened habitat, and species endemic to this environment are under extreme pressure. The tree species, Lonchocarpus costaricensis is endemic to the dry northwest of Costa Rica and southwest Nicaragua. It is a locally important species but, as land has been cleared for agriculture, populations have experienced considerable reduction and fragmentation. To assess current levels and distribution of genetic diversity in the species, a combination of chloroplast-specific (cpDNA) and whole genome DNA markers (amplified fragment length polymorphism, AFLP) were used to fingerprint 121 individual trees in 6 populations. Two cpDNA haplotypes were identified, distributed among populations such that populations at the extremes of the distribution showed lowest diversity. A large number (487) of AFLP markers were obtained and indicated that diversity levels were highest in the two coastal populations (Cobano, Matapalo, H = 0.23, 0.28 respectively). Population differentiation was low overall, F ST = 0.12, although Matapalo was strongly differentiated from all other populations (F ST = 0.16-0.22), apart from Cobano (F ST = 0.11). Spatial genetic structure was present in both datasets at different scales: cpDNA was structured at a range-wide distribution scale, whilst AFLP data revealed genetic neighbourhoods on a population scale. In general, the habitat degradation of recent times appears not to have yet impacted diversity levels in mature populations. However, although no data on seed or saplings were collected, it seems likely that reproductive mechanisms in the species will have been affected by land clearance. It is recommended that efforts should be made to conserve the extant genetic resource base and further research undertaken to investigate diversity levels in the progeny generation.
Molecular Ecology, 2003
Habitat fragmentation represents the single most serious threat to the survival of tropical ecosystems. In formulating strategies to counteract the detrimental effects of fragmentation, knowledge of the levels and patterns of genetic diversity within and between natural populations is vital to the establishment of any conservation programme. We utilized polymorphic chloroplast microsatellite markers to analyse genetic diversity in populations of the endangered tropical tree Caesalpinia echinata Lam. representing the entire extant range of the species. Levels of within-population diversity were low, with only two of seven populations studied displaying any variation. The vast majority of the genetic variation was partitioned between geographical regions (36%) and between populations within regions (55%). These levels of genetic structuring, coupled with a calculated pollen-to-seed flow ratio of ≈ ≈ ≈ ≈ 6.7:1, suggest that there has been little gene flow between the three major geographical regions over an extended period. Thus, the current tripartite distribution of the species is more consistent with the existence of separate glacial refugia, rather than reflecting any anthropogenic effects.
Genetic variation and phylogeography of tree species from North and Southeast Asia
CHAPTER 1 Phylogeography of Larix sukaczewii Dyl. and L. sibirica L. inferred from nucleotide variation of nuclear genes. The phylogeography of Larix sukaczewii and L. sibirica was investigated using nucleotide variation at the four following nuclear gene regions: 5.8S rDNA (including two internal transcribed spacers (ITS)), glyoxysomal malate dehydrogenase (gMDH), cinnamyl alcohol dehydrogenase (CAD) and phytochrome-O (PHYO). Sequences of the 4-coumarate: coenzyme A ligase (4CL) gene region obtained in a recent study were also included. CAD and PHYO showed very low nucleotide variation, but ITS, 4CL and gMDH had levels of variation similar to those reported for other conifers. Neutrality tests showed significant deviations at the gMDH region. Namely, positive values of Tajima’s D, Fu and Li’s D and F (with and without outgroup) were observed in all but one population of L. sukaczewii, but negative values were observed in all populations of L. sibirica. Pleistocene refugia have been hypothesized to exist in the southern Urals and south-central Siberia, where four out of nine of the investigated populations occur. Moderate to high levels of population differentiation were found in some pair-wise comparisons suggesting limited gene flow and independent evolution of some refugial populations. In L. sukaczewii, low levels of differentiation were found among populations from areas glaciated during the Pleistocene, indicating their recent origin. Results of this study also suggest these populations were created by migrants from multiple, genetically distinct refugia. Furthermore, some haplotypes observed in populations from previously glaciated areas were not found in putative refugial ones, suggesting these populations might have contributed little to the extant populations created after the Last Glacial Maximum (LGM). Some authors regard L. sukaczewii and L. sibirica as a single species, while others consider them as separate species. The observed conspicuous differences in haplotype composition and distribution between L. sukaczewii and L. sibirica, together with high values of FST between populations of the two species appear to support the latter classification. -------------------------------------------------------------------------------------- CHAPTER 2 Genetic structure of Dipterocarpus alatus Roxb. populations from Thailand revealed by nuclear microsatellites. Four populations of Dipterocarpus alatus from Thailand using nuclear microsatellite loci were investigated. Two populations were from mainland Thailand, one from Samui Island and one from Malay Peninsula. Nine pairs of primers originally designed for the related species Shorea curtisii were tested. However, only four loci were successfully amplified; and only two of them (Shc02 and Shc07) were polymorphic. Null alleles appeared to be present at the Shc07 locus, but significant deviations from HWE was found only in Samui population at this locus. Levels of genetic variation observed in D. alatus were similar to those revealed in other studies on tropical trees using microsatellites. The levels of population differentiation (FST and RST) for microsatellites were lower than those observed for isozymes in another study on D. alatus that included three out of four populations investigated in this study. Genetic distances; however, were generally consistent between microsatellites and isozymes in pair-wise comparisons, except between Kuphrakona (mainland) and Hat Yai (Malay Peninsula), where microsatellite results suggested these two geographically distant populations were relatively close to each other, but isozymes suggested the opposite. This discrepancy could have been caused by homoplasy at microsatellite loci in these two populations. The genetic distances showed that Hat Yai was the most isolated population indicating it has been isolated for a relatively long period of time. The two mainland populations were closer to each other and the population from Samui had an intermediate position between mainland and Hat Yai, in genetic distances, which is consistent with its geographical position. Therefore, gene flow could have occurred between Samui and other populations in the past.