Amplified fragment length polymorphism (AFLP) analysis of genetic variation in Moringa oleifera Lam

Research on Moringa (Moringa oleifera Lam.) in Africa

While Moringa oleifera Lam. is gaining importance in Africa, especially sub-Saharan Africa, it is unclear whether research is following the quick pace of its development on the continent. Therefore, this article analyzes the landscape of research dealing with moringa in Africa. This systematic review draws upon 299 eligible articles identified through a search carried out on the Web of Science in April 2023. Research on M. oleifera is rather recent in Africa but interest is increasing among scholars. While the research field is multidisciplinary and cross-sectoral, the literature seems to focus on biological and environmental sciences. Moreover, research is performed mainly in South Africa, Nigeria, Egypt, and Ghana. The analysis suggests a significant potential contribution of moringa to food security and nutrition, climate change mitigation/adaptation, farming systems resilience, and livelihoods. Its versatility and diverse applications and uses make moringa particularly interesting for developing countries, such as African ones. However, this review also underscores some factors hindering its development. Therefore, there is a need to strengthen research on moringa to unlock its potential in Africa. Investments in research, innovation, and development can help address the many challenges that Africa faces and contribute to the transition towards sustainable and resilient food systems.

Miracle Tree Moringa oleifera: Status of the Genetic Diversity, Breeding, In Vitro Propagation, and a Cogent Source of Commercial Functional Food and Non-Food Products

Moringa oleifera Lam. (MO) is a fast-growing drought-resistant tree belonging to the family Moringaceae and native to the Indian subcontinent and cultivated and/or naturalized worldwide with a semi-arid climate. MO is also popularly known as a miracle tree for its repertoire of nutraceutical, pharmacological, and phytochemical properties. The MO germplasm is collected, conserved, and maintained by various institutions across the globe. Various morphological, biochemical, and molecular markers are used for determining the genetic diversity in MO accessions. A higher yield of leaves and pods is often desirable for making various products with commercial viability and amenable for trade in the international market. Therefore, breeding elite varieties adapted to local agroclimatic conditions and in vitro propagation are viable and sustainable approaches. Here, we provide a comprehensive overview of MO germplasm conservation and various markers that are employed for assessing the genetic diversity among them. Further, breeding and in vitro propagation of MO for various desirable agronomic traits are discussed. Finally, trade and commerce of various functional and biofortified foods and non-food products are enumerated albeit with a need for a rigorous and stringent toxicity evaluation.

Health benefits and phenolic compounds of Moringa oleifera leaves: A comprehensive review

BACKGROUND

Moringa oleifera Lam (MO) is native to India and is a cash crop widely cultivated in tropical and sub-tropical areas. The health improving properties of MO has been studied from a long time ago for the numerous phenolic compounds, including vitamins, flavonoids, phenolic acids, isothiocyanates, tannins and saponins, which are present in considerable amounts in the plant. A growing spectrum of therapeutic characteristics of MO leaves has been found and used in the remission or treatment of oxidative stress, liver disease, neurological disease, hyperglycemia and cancer.

HYPOTHESIS

This review focused on researches applying MO or MO leaf extract as a functional food or cure against various disease and cellular injuries. We believed it would help the discovery of therapeutic application of MO and understanding of MO phytochemistry.

METHODS

The data collected in this review were extracted from researches indexed in Web of Science, google scholar, PubMed, Science Direct and Scopus to find out health benefits and biological activities of MO leaves polyphenols. The studies reporting mechanistic route of phenolic compounds of MO leaves were also considered in the present study.

RESULTS

It has been reported that polyphenols of MO leaf have protective characteristics against neurodegenerative disorders through reducing DNA damage, activation of AchE activity and inhibition of caspase-3 activity. It has been reported that, they protected the kidney from damage caused by melamine through suppressed the pro-inflammatory cytokine, metallopeptidase inhibitor 1 (TIMP-1), and kidney injury molecule 1 (KIM-1). Similarly, methanol extract of MO leaves has low hypoglycemic attributes and attenuate the risk of diabetes caused by alloxan by enhancing lipid metabolism and stimulating insulin release, glucose uptake, and glycogen synthesis. In addition, MO leaves are becoming the best phytomedicine to reduce hypertension, which are naturally known as angiotensin-1converting enzyme (ACE), acetylcholinesterase, arginase and phosphodiesterase 5 (PDE5) inhibitors.

CONCLUSION

MO leaves extract as a health promoting food additives for human and animals due to its great protective effect against many diseases and the widely persistent environmental toxins which disrupted cellular metabolic function. More studies are required to use the phenolic compounds of MO leaves to develop and produce drugs for controlling and treatment of various diseases.

Phenotypic plasticity of two M. oleifera ecotypes from different climatic zones under water stress and re-watering

Moringa oleifera is a fast-growing hygrophilic tree native to a humid sub-tropical region of India, now widely planted in many regions of the Southern Hemisphere characterized by low soil water availability. The widespread cultivation of this plant worldwide may have led to populations with different physiological and biochemical traits. In this work, the impact of water stress on the physiology and biochemistry of two M. oleifera populations, one from Chaco Paraguayo (PY) and one from Indian Andhra Pradesh (IA) region, was studied in a screenhouse experiment where the water stress treatment was followed by re-watering. Through transcriptome sequencing, 2201 potential genic simple sequence repeats were identified and used to confirm the genetic differentiation of the two populations. Both populations of M. oleifera reduced photosynthesis, water potential, relative water content and growth under drought, compared to control well-watered plants. A complete recovery of photosynthesis after re-watering was observed in both populations, but growth parameters recovered better in PY than in IA plants. During water stress, PY plants accumulated more secondary metabolites, especially β-carotene and phenylpropanoids, than IA plants, but IA plants invested more into xanthophylls and showed a higher de-epoxidation state of xanthophylls cycle that contributed to protect the photosynthetic apparatus. M. oleifera demonstrated a high genetic variability and phenotypic plasticity, which are key factors for adaptation to dry environments. A higher plasticity (e.g. in PY plants adapted to wet environments) will be a useful trait to endure recurrent but brief water stress episodes, whereas long-term investment of resources into secondary metabolism (e.g. in IA plants adapted to drier environments) will be a successful strategy to cope with prolonged periods of drought. This makes M. oleifera an important resource for agro-forestry in a climate change scenario.

The efficiency of Cytochrome P450 gene-based markers in accessing genetic variability of drumstick (Moringa oleifera Lam.) accessions

Drumstick (Moringa oleifera Lam.) is an important vegetable as well as forage crop of arid and semi-arid zones of the tropics. The leaves and pods of the plant are rich sources of minerals and vitamins. In the present work, genetic diversity study of 23 genotypes of M. oleifera collected from Kerala, Tamil Nadu and Karnataka states of India was carried out using seven cytochrome P450 (CytP450) markers. By using seven pairs of CytP450 gene-based markers, 88.25% of polymorphism was recorded among the 23 sampled genotypes. The Polymorphic Information Content (PI), Marker Index (MI) and Resolving Power obtained for seven primers were estimated 0.23, 2.96 and 9.83, respectively. The Unweighted Pair Group Method with Arithmetic mean (UPGMA) dendrogram based on this marker data indicate that genotypes from different geographical regions are placed in the same clusters. The dendrogram and Principal Coordinates Analysis (PCoA) plots derived from the binary data matrices were highly concordant. The investigation, in brief, proved that CytP450 based marker system is efficient in the elucidation of genetic diversity in M. oleifera accessions.

Cultivation, Genetic, Ethnopharmacology, Phytochemistry and Pharmacology of Moringa oleifera Leaves: An Overview

Moringa oleifera is an interesting plant for its use in bioactive compounds. In this manuscript, we review studies concerning the cultivation and production of moringa along with genetic diversity among different accessions and populations. Different methods of propagation, establishment and cultivation are discussed. Moringa oleifera shows diversity in many characters and extensive morphological variability, which may provide a resource for its improvement. Great genetic variability is present in the natural and cultivated accessions, but no collection of cultivated and wild accessions currently exists. A germplasm bank encompassing the genetic variability present in Moringa is needed to perform breeding programmes and develop elite varieties adapted to local conditions. Alimentary and medicinal uses of moringa are reviewed, alongside the production of biodiesel. Finally, being that the leaves are the most used part of the plant, their contents in terms of bioactive compounds and their pharmacological properties are discussed. Many studies conducted on cell lines and animals seem concordant in their support for these properties. However, there are still too few studies on humans to recommend Moringa leaves as medication in the prevention or treatment of diseases. Therefore, further studies on humans are recommended.

Genomic profile of the plants with pharmaceutical value

There is an ample genetic diversity of plants with medicinal importance around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, identification, characterization and documentation of the gene pool of medicinal plants are essential for this purpose. Genomic information of many a medicinal plant species has increased rapidly since the past decade and genetic resources available for domestication and improvement programs include genome sequencing, expressed sequence tags sequencing, transcript profiling, gene transmit, molecular markers in favor of mapping and breeding. In recent years, multiple endeavors have been undertaken for genomic characterization of medicinal plant species with the aid of molecular markers for sustainable utilization of gene pool, its conservation and future studies. Recent advancement in genomics is so fast that only some researches have been published till date and to a large extent documentation is restricted to electronic resources. Whole genome profiling of the identified medicinal plant species, carried out by several researchers, based on the DNA fingerprinting, is well documented in the present review. This review will facilitate preparing a database of the widely used, economically important medicinal plant species, based on their genomic organization.

QTL scanning for rice yield using a whole genome SNP array

High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line (RIL) population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length of 1.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.

Phylogeography of North American herbaceous Smilax (Smilacaceae): Combined AFLP and cpDNA data support a northern refugium in the Driftless Area

PREMISE OF THE STUDY

The genetic structure of North American herbaceous Smilax, a clade of closely related understory herbs that has a wide and disjunct distribution, was investigated to test the hypothesis of whether a northern refugium in the upper Midwest may have existed for these plants during the last glaciation.

METHODS

We analyzed 33 populations sampled from California and throughout the eastern United States using AFLP and chloroplast DNA sequence data.

KEY RESULTS

Individuals of S. jamesii from northern California formed a clade sister to the eastern North American species, and they likely diverged from each other during the Pleistocene. Among the eastern species, two lineages were found on opposite sides of the Appalachian Mountains. The populations near the "Driftless Area" contained most of the chlorotypes found in the Midwest, including a unique one endemic to this area, and the AFLP data indicated that one population from this area has the highest frequency-down-weighted-marker value.

CONCLUSIONS

This study, and others that have focused on mammals, amphibians, and woody plants, provides further evidence for the debate over whether the upper Midwest's "Driftless Area" may have hosted a biologically diverse northern glacial refugium. Herbaceous species of Smilax from eastern North American exhibit an Appalachian discontinuity. They appear to have persisted in multiple refugia both east and west of the Appalachians, with several populations persisting in situ through the Last Glacial Maximum (LGM). We suggest that they experienced localized expansion after the LGM, possibly followed by subsequent contact between the Midwest and the East Coastal lineages.

Plio-Pleistocene history and phylogeography of Acacia senegal in dry woodlands and savannahs of sub-Saharan tropical Africa: evidence of early colonisation and recent range expansion

Drylands are extensive across sub-Saharan Africa, socio-economically and ecologically important yet highly sensitive to environmental changes. Evolutionary history, as revealed by contemporary intraspecific genetic variation, can provide valuable insight into how species have responded to past environmental and population changes and guide strategies to promote resilience to future changes. The gum arabic tree (Acacia senegal) is an arid-adapted, morphologically diverse species native to the sub-Saharan drylands. We used variation in nuclear sequences (internal transcribed spacer (ITS)) and two types of chloroplast DNA (cpDNA) markers (PCR-RFLP, cpSSR) to study the phylogeography of the species with 293 individuals from 66 populations sampled across its natural range. cpDNA data showed high regional and rangewide haplotypic diversity (h(T(cpSSR))=0.903-0.948) and population differentiation (G(ST(RFLP))=0.700-0.782) with a phylogeographic pattern that indicated extensive historical gene flow via seed dispersal. Haplotypes were not restricted to any of the four varieties, but showed significant geographic structure (G(ST(cpSSR))=0.392; R(ST)=0.673; R(ST)>R(ST) (permuted)), with the major division separating East and Southern Africa populations from those in West and Central Africa. Phylogenetic analysis of ITS data indicated a more recent origin for the clade including West and Central African haplotypes, suggesting range expansion in this region, possibly during the Holocene humid period. In conjunction with paleobotanical evidence, our data suggest dispersal to West Africa, and across to the Arabian Peninsula and Indian subcontinent, from source populations located in the East African region during climate oscillations of the Plio-Pleistocene.

Genetic diversity in inter-simple sequence repeat profiles across natural populations of Indian pomegranate (Punica granatum L.)

Pomegranate (Punica granatum L.), in the monogeneric family Punicaceae, is found in Iran, Afghanistan, India and Mediterranean countries. Iran is considered to be its primary centre of origin. In India, pomegranate occurs naturally only in the Western Himalayan regions of Jammu and Kashmir, Himachal Pradesh and Uttarakhand States. However, there is no information about genetic variation in wild pomegranate at population level. In this paper, we describe genetic diversity across natural populations of Indian pomegranate based on inter-simple sequence repeat (ISSR) markers. Forty-nine accessions representing eight populations from two regions were analysed using ISSR. Seventeen ISSR primers resulted in 268 polymorphic bands, with 87.01% polymorphism throughout the accessions. Pair-wise population genetic distances ranged from 0.05 to 0.45, with a mean of 0.25 between populations. amova and Nei's genetic diversity analyses revealed higher genetic variation within populations than among populations. A higher genetic differentiation (G(ST)) was observed between the spatially distant populations, indicating a low level of genetic exchange (Nm) among these populations. However, clustering of populations was not in accordance with their geographical affiliations in the tree. The results indicate that the ISSR method is sufficiently informative and powerful to assess genetic variability in pomegranate, and that patterns of genetic variability observed among populations of wild pomegranate from the Western Himalaya differ. Estimation of genetic variation reported here provides a significant insight for in situ conservation and exploitation of genetic resources for this economically important species as potential breeding material.

Phylogenetic relationships and natural hybridization among the North American woody bamboos (Poaceae: Bambusoideae: Arundinaria)

In spite of the ecological and economic importance of temperate bamboos, relatively little is known about their population biology or evolutionary history. Recently, hybridization has emerged as a potential source of diversity in this group, as well as an underlying cause of taxonomic problems. As part of a broader phylogenetic study of the temperate bamboos, we report the results of an analysis of the North American Arundinaria gigantea species complex, including estimates of genetic variation and molecular evidence of natural hybridization among A. gigantea, A. tecta, and A. appalachiana. The study involved a comparative analysis of amplified fragment length polymorphisms (AFLPs) and chloroplast DNA sequences representing diversity within and among all three species plus individuals with intermediate or unusual morphological characteristics (putative hybrids). Molecular results support the recognition of three species previously defined on the basis of morphology, anatomy, and ecology, with most of the molecular variance accounted for by among-species variation. Molecular evidence also demonstrates that A. tecta and A. appalachiana are sister species, forming a clade that is significantly divergent from A. gigantea. The role of hybridization in the phylogenetic history of Arundinaria is discussed along with implications for the evolution and taxonomy of the temperate woody bamboos.

Genetic analysis and historical perspective of cashew (Anacardium occidentaleL.) introduction into India

Cashew ( Anacardium occidentale L.), introduced into India about 400 years ago, is distributed widely in the coastal regions as spontaneous populations as well as in cultivation. Despite the plant’s commercial exploitation, little is known about its actual introduction and diversification. We attempted to construct these events by investigating the level of genetic variation and genetic structure of cashew populations collected from different geographical regions of India. A total of 91 individuals from four populations were analysed using AFLP markers and morphometric data. AFLP analysis based on 354 polymorphic loci revealed Indian cashew to have low but relatively substantial genetic diversity for an introduced species (HE = 0.262 and IS = 0.404). Twenty-seven qualitative and quantitative traits also revealed the existence of considerable morphometric variation (24% around the mean values). Bayesian cluster analysis based on AFLP data did not indicate the existence of definite population differentiation. Morphometric analysis allocated 12% variation among all four populations, whereas AFLP variation observed in cashew individuals was entirely within populations. The results, supporting the possibility of cashew having been introduced into India repeatedly over a period of time but at a single location (west coast), are discussed and their implications for germplasm management are described.

Phylogeography of a specialist insect, Adelges cooleyi: historical and contemporary processes shape the distribution of population genetic variation

Adelges cooleyi is a host-alternating, gall-making insect native to the Rocky Mountains and Cascade Mountains in western North America. The insect's primary hosts are Picea (spruce) species, and its secondary host is Pseudotsuga menziesii, Douglas fir. To determine whether there are large-scale patterns of genetic variation in this specialist insect, we created molecular phylogenies of geographically separate samples of A. cooleyi using sequence data from two mitochondrial (mtDNA) genes and amplified fragment length polymorphisms (AFLPs). Three divergent mtDNA lineages were identified. Analysis of mtDNA and AFLP genetic variation revealed that samples from southeastern Arizona are genetically isolated from all other samples. AFLP data identified possible gene flow between individuals from divergent mtDNA lineages in an area in the central Rocky Mountains. Factors that likely affected divergence within A. cooleyi were identified by comparing our conclusions with well-known changes in the distribution of vegetation in response to glaciations and previous phylogeographical work conducted on this specialist insect's host-plants. In addition to documenting previously unknown patterns of genetic variation in A. cooleyi, our work provides the basis for a testable hypothesis regarding the extent to which the distribution of variation in Picea and Pseudotsuga hosts mediates the distribution of genetic variation for this specialist insect.

Ecological risk assessment using RAPD and distribution pattern of a rare and endangered species

Environmental and ecological risk assessment always provide useful evidence for characterisation and conservation of the rare and endangered species, e.g. seven-son flower (Heptacodium miconioides Rehd.). Seven-son flower is a deciduous arbor species, but endangered, with a restricted distribution in the subtropical forests of China. Genetic risk assessment of 56 samples of the flower from nine main populations in Zhejiang (China) was carried out by using the RAPD analysis. This was to study the ecological characteristics, spatial distribution and genetic features of the seven-son flower communities and establish a feasible conservation plan. Twenty-one primers screened from 50 yielded 119 RAPD bands with 72 polymorphic products and 60.50% of total bands. The genetic variation was found to be partitioned mainly among rather than within populations. Percentages of genetic diversity among populations were quantified by Shannon index and the Nei's gene diversity coefficient. AMOVA also demonstrated that these relict populations were highly differentiated. The high level of population variation observed is in contrast to that expected for a primarily outcrossed woody perennial plant, and suggests that there may be a degree of inbreeding. The dendrogram constructed from genetic distances through UPGMA method based on Nei's coefficients shows two groups among nine population clusters, which is further supported by a principle components analysis (PCA) of RAPD phenotypic data. The analysis showed that the biologic characteristics and habitat fragmentation were the reasons of the great genetic variation among populations. Some strategies of its genetic diversity conservation were proposed in the fragmented habitats based on its genetic structure and its biological characteristics in this study.

Optimization of bulked AFLP analysis and its application for exploring diversity of natural and cultivated populations of red clover

Landraces and wild populations of red clover (Trifolium pratense L.) may represent a significant yet poorly characterized genetic resource of temperate grasslands. A bulking strategy with amplified fragment length polymorphism (AFLP) markers was optimized to characterize 120 red clover populations in 6 different groups: Swiss wild clover populations, Mattenklee landraces, Mattenklee cultivars, field clover cultivars, Dutch wild clover populations, and Dutch landraces. Analysis of 2 bulked samples/population consisting of 20 plants each with12 AFLP primer combinations was found optimal for determining genetic diversity and relationships within and among red clover populations and groups. Swiss wild clover populations were clearly separated from all other red clover groups and variability within and among populations was shown to be particularly high in wild clover populations and Mattenklee landraces, emphasising their value as genetic resources for improvement of red clover cultivars, as well as for conservation and restoration of biodiversity. This study shows that the ancestry of red clover landraces is primarily found in introduced cultivars rather than in natural wild clover populations. In addition, the methodological considerations presented here may help improve diversity analyses using bulked samples.

Do farmers reduce genetic diversity when they domesticate tropical trees? A case study from Amazonia

Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high.

Genetic diversity and biogeography of Cunninghamia konishii (Cupressaceae), an island species in Taiwan: a comparison with Cunninghamia lanceolata, a mainland species in China

Luanta-fir (Cunninghamia konishii), an endemic to Taiwan, is an outcrossing, long-lived conifer. Populations of C. konishii are generally fragmented due to a once high intensity of timber exploitation. C. konishii and Cunninghamia lanceolata are two sibling taxa constituting derivative-progenitor species relationship. The amount of genetic variations within and between 11 and 10 populations of C. konishii and C. lanceolata, respectively, were assessed using amplified fragment length polymorphism (AFLP) markers in this report. Three AFLP primer pairs generated a total of 357 and 226 markers for C. konishii and C. lanceolata samples, of which 56.1 and 65.3% are polymorphic, respectively. Analysis of molecular variance indicates a 4.78% variation between C. konishii and C. lanceolata. A relatively high value of genetic variation (24.60%) was apportioned between the populations of C. konishii. In contrast, a lower divergence value (12.21%) between populations was found for C. lanceolata. The population with the highest genetic diversity was found in Nantou County, which concurred with the results of many other tree species investigated in Taiwan. The estimates of the number of migrants between populations (Nm), obtained from population pair-wise PhiST, suggest that gene flow in C. konishii is efficient in some adjacent populations but is restricted in the rest. Individual UPGMA tree, generated based on AFLP markers, suggests six evolutionary lineages for C. konishii. All evolutionary lineages of C. konishii were derived from C. lanceolata. In conclusion, the migration patterns of Cunninghamia from mainland China may have been established following multiple sources, migrant-pools, long-distance dispersal events, and via different directions.

Differentiation in a geographical mosaic of plants coevolving with ants: phylogeny of the Leonardoxa africana complex (Fabaceae: Caesalpinioideae) using amplified fragment length polymorphism markers

Comprising four allopatric subspecies that exhibit various grades of ant-plant interactions, from diffuse to obligate and symbiotic associations, the Leonardoxa africana complex (Fabaceae, Caesalpinioideae) provides a good opportunity to investigate the evolutionary history of ant-plant mutualisms. A previous study of the L. africana complex based on chloroplast DNA noncoding sequences revealed a lack of congruence between clades suggested by morphological and plastid characters. In this study, we analysed phylogenetic relationships within the L. africana complex using a Bayesian probability approach on amplified fragment length polymorphism markers. The results reported permit partial validation of the four subspecies of L. africana previously defined by morphological and ecological markers. Incongruences between phylogenies based on chloroplast DNA and amplified fragment length polymorphism markers are discussed in the light of morphological and ecological data, and confronted with hypotheses of convergence, lineage sorting and introgression.

Genetic variation of Trigonobalanus verticillata, a primitive species of Fagaceae, in Malaysia revealed by chloroplast sequences and AFLP markers

The genetic variation of Trigonobalanus verticillata, the most recently described genus of Fagaceae, was studied using chloroplast DNA sequences and AFLP fingerprinting. This species has a restricted distribution that is known to include seven localities in tropical lower montane forests in Malaysia and Indonesia. A total of 75 individuals were collected from Bario, Kinabalu, and Fraser's Hill in Malaysia. The sequences of rbcL, matK, and three non-coding regions (atpB-rbcL spacer, trnL intron, and trnL-trnF spacer) were determined for 19 individuals from these populations. We found a total of 30 nucleotide substitutions and four length variations, which allowed identification of three haplotypes characterizing each population. No substitutions were detected within populations, while the tandem repeats in the trnL -trnF spacer had a variable repeat number of a 20-bp motif only in Kinabalu. The differentiation of the populations inferred from the cpDNA molecular clock calibrated with paleontological data was estimated to be 8.3 MYA between Bario and Kinabalu, and 16.7 MYA between Fraser's Hill and the other populations. In AFLP analysis, four selective primer pairs yielded a total of 431 loci, of which 340 (78.9%) were polymorphic. The results showed relatively high gene diversity (H(S) = 0.153 and H(T) = 0.198) and nucleotide diversity (pi(S) = 0.0132 and pi(T) = 0.0168) both within and among the populations. Although the cpDNA data suggest that little or no gene flow occurred between the populations via seeds, the fixation index estimated from AFLP data (F(ST) = 0.153 and N(ST) = 0.214) implies that some gene flow occurs between populations, possibly through pollen transfer.

Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size

We investigate the distribution of sizes of fragments obtained from the amplified fragment length polymorphism (AFLP) marker technique. We find that empirical distributions obtained in two plant species, Phaseolus lunatus and Lolium perenne, are consistent with the expected distributions obtained from analytical theory and from numerical simulations. Our results indicate that the size distribution is strongly asymmetrical, with a much higher proportion of small than large fragments, that it is not influenced by the number of selective nucleotides nor by genome size but that it may vary with genome-wide GC-content, with a higher proportion of small fragments in cases of lower GC-content when considering the standard AFLP protocol with the enzyme MseI. Results from population samples of the two plant species show that there is a negative relationship between AFLP fragment size and fragment population frequency. Monte Carlo simulations reveal that size homoplasy, arising from pulling together nonhomologous fragments of the same size, generates patterns similar to those observed in P. lunatus and L. perenne because of the asymmetry of the size distribution. We discuss the implications of these results in the context of estimating genetic diversity with AFLP markers.

Random amplified polymorphic DNA and amplified fragment length polymorphism assessment of genetic variation in Nicaraguan populations of Pinus oocarpa

Pinus oocarpa is the most widely distributed pine species of Mexico and Central America. The natural populations of Nicaragua have been affected by extensive human activities. As a consequence, their size has been reduced, and there is a serious threat to the development of mature woodland. Knowledge of population structures and the genetic diversity of the species is required for the design of sustainable use and conservation strategies. Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers were used to assess the genetic variation among 10 populations from three geographical regions of Nicaragua. Both markers revealed high levels of diversity in these populations. G(ST) values and analyses of molecular variance (AMOVA) found that most variation was within populations but there is still a significant differentiation between populations indicating that the populations sampled cannot be considered a single panmictic unit. The partitions created by AMOVA also showed that there was little differentiation between populations of different regions, although cluster analyses based on RAPDs and AFLPs indicated a closer relationship among most of the populations from a same geographical region. Management of P. oocarpa in Nicaragua should be aimed to maintain the high degree of genetic variation within individual populations that is still observed even in some of these highly degraded populations.

Conservation genetics of the rare and endangered Leucopogon obtectus (Ericaceae)

Leucopogon obtectus Benth. is a declared rare species found in the kwongan vegetation in Western Australia. Plants on a mineral sand mine and the rehabilitation area are subject to disturbance. Genetic diversity was examined within and among all known populations using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphisms (AFLPs) for conservation. Both molecular markers revealed a high percentage (> 89%) of polymorphic markers and a high mean genetic distance among individuals (D = 0.3). Analysis of molecular variance showed that 86.7% (RAPD) and 89.7% (AFLP) of variability was partitioned among individuals within populations. Exact tests showed no significant population differentiation. The analyses indicated that L. obtectus exhibits high levels of genetic diversity despite small population sizes. The high levels of variability among individuals and the lack of clear population differentiation suggest that this species comprises a single, genetically diverse group. Conservation and management of L. obtectus should concentrate on maintaining the high levels of genetic variability through mixing genotypes and promoting outcrossing.

Geographical patterns of genetic variation in two species of Stylosanthes Sw. using amplified fragment length polymorphism

Understanding the extent and distribution of genetic diversity within a species is essential for the development of effective conservation strategies. The objective of this study was to assess genetic variation using amplified fragment length polymorphisms (AFLP) in two species of the tropical legume genus Stylosanthes Sw. Annual, S. humilis (2n = 20) and perennial, S. viscosa (2n = 20) are found throughout tropical America, and are sympatric for much of their range of distribution. One hundred and eleven accessions, covering a wide geographical range, were selected for AFLP analysis. Binary data matrices derived from DNA banding patterns were analysed using the software programs NTSYS-PC and ARLEQUIN. Several accessions were found to be misidentified. Of the S. humilis accessions, the overall average similarity value was (0.72) slightly higher than the value obtained for S. viscosa (0.67). Cluster analysis and principal coordinate analysis grouped accessions from both species by geographical origin, with a few exceptions. Analysis of molecular variance (AMOVA) in S. humilis revealed 59.4% of the variation among groups formed from the cluster analysis. This was highly significant (P < 0.001). For S. viscosa AMOVA also revealed more variation among than within groups (66.5%). This was also highly significant (P < 0.001). The majority of accessions of both species conserved ex situ are of Brazilian and Venezuelan origin. This study has identified areas in Central America and Mexico for which novel genetic variation may be found and where conservation activities should be focused.

Resistance or emigration: response of the high-alpine plant Eritrichium nanum (L.) Gaudin to the ice age within the Central Alps

Two main possibilities regarding glacial survival of the mountain flora of the Alps during the Quaternary have been discussed: the tabula rasa and the nunatak hypotheses. Eritrichium nanum (L.) Gaudin (Boraginaceae) is a perennial cushion plant, occurring at high elevations of the Central Alps and having a preference for extreme habitats. It belongs to a group of high-alpine plants, for which in situ glacial survival on nunataks is ecologically possible. By investigating 20 populations of E. nanum of potential nunatak and peripheral refugial regions using amplified fragment length polymorphism, considerable genetic differences between populations from the Central Alps and populations from peripheral refugia were detected; hence, the latter probably did not serve as potential sources for the re-colonization of the Central Alps after glaciation. Genetic variation was hierarchically structured (AMOVA), and three genetically distinct regions could be identified in the Central Alps. Two of these, the Penninic and Rhaetic Alps, correspond to nunatak regions proposed in the biogeographic literature. Populations from the Lepontic Alps formed a third genetic group. Genetic correlation (Mantel statistics) was highest within populations, with a modest decline among populations within specific nunatak regions and a negative correlation outside the genetic influence of specific nunatak regions. In situ glacial survival in E. nanum could be a model for the Quaternary history of other alpine plants, especially those that also occur at high elevations and in similar habitats.

Genetic differentiation of Euterpe edulis Mart. populations estimated by AFLP analysis

Heart-of-palm (Euterpe edulis Mart.) is a wild palm with a wide distribution throughout the Atlantic Rainforest. Populations of E. edulis represent important renewable natural resources but are currently under threat from predatory exploitation. Furthermore, because the species is indigenous to the Atlantic Rainforest, which is located in the most economically developed and populated region of Brazil, social and economic pressures have devastated heart-of-palm forests. In order to estimate the partitioning of genetic variation of endangered E. edulis populations, 429 AFLP markers were used to analyse 150 plants representing 11 populations of the species distribution range. Analysis of the genetic structure of populations carried out using analysis of molecular variance (AMOVA) revealed moderate genetic variation within populations (57. 4%). Genetic differentiation between populations (FST = 0.426) was positively correlated with geographical distance. These results could be explained by the historical fragmentation of the Atlantic coastal region, together with the life cycle and mating system. The data obtained in this work should have important implications for conservation and future breeding programmes of E. edulis.

Genetic diversity in an endangered alpine plant, Eryngium alpinum L. (Apiaceae), inferred from amplified fragment length polymorphism markers

Eryngium alpinum L. is an endangered species found across the European Alps. In order to obtain base-line data for the conservation of this species, we investigated levels of genetic diversity within and among 14 populations from the French Alps. We used the amplified fragment length polymorphism (AFLP) technique with three primer pairs and scored a total of 62 unambiguous, polymorphic markers in 327 individuals. Because AFLP markers are dominant, within-population genetic structure (e.g. FIS) could not be assessed. Analyses based either on the assumption of random-mating or on complete selfing lead to very similar results. Diversity levels within populations were relatively high (mean Nei's expected heterozygosity = 0.198; mean Shannon index = 0.283), and a positive correlation was detected between both genetic diversity measurements and population size (Spearman rank correlation: P = 0. 005 and P = 0.002, respectively). Moreover, FST values and exact tests of differentiation revealed high differentiation among populations (mean pairwise FST = 0.40), which appeared to be independent of geographical distance (nonsignificant Mantel test). Founder events during postglacial colonizations and/or bottlenecks are proposed to explain this high but random genetic differentiation. By contrast, we detected a pattern of isolation by distance within populations and valleys. Predominant local gene flow by pollen or seed is probably responsible for this pattern. Concerning the management of E. alpinum, the high genetic differentiation leads us to recommend the conservation of a maximum number of populations. This study demonstrates that AFLP markers enable a quick and reliable assessment of intraspecific genetic variability in conservation genetics.

Genetic analysis and conservation of 31 surviving individuals of a rare New Zealand tree, Metrosideros bartlettii (Myrtaceae)

Metrosideros bartlettii (Myrtaceae) is a distinctive and extremely rare tree, endemic to New Zealand, first discovered in 1975. Prior to this study, a total of 19 adult individuals of the species had been reported; these are located in three small forest remnants in the far north of the North Island of New Zealand. Here we describe a total of 31 adult M. bartlettii at the three sites, including 12 individuals newly discovered by us. We analyse the genetic diversity of the species, using microsatellites to examine the chloroplast genome and amplified fragment length polymorphisms (AFLPs) to monitor nuclear variation. The results clearly demonstrate that M. bartlettii is a unique species, distinct from its two closest relatives M. robusta and M. excelsa. Analysis of genetic diversity within the 31 remaining individuals of M. bartlettii showed an average heterozygosity (< H >) of 0.18 and a proportion of polymorphic genes (< P >) of 0.44. Population structure, as shown by 286 AFLP loci, varied between the three geographical sites; the site with fewest individuals, containing two trees, showed some separation from the populations at the other two locations. These two latter sites, by contrast, had highly overlapping AFLP population diversity profiles. The implications of these results for conservation of the species are discussed.