ISSR-PCR: tool for discrimination and genetic structure analysis of Plutella xylostella populations native to different geographical areas

The diamondback moth (DBM), Plutella xylostella (L.) is considered as the most destructive pest of Brassicaceae crops world-wide. Its migratory capacities and development of insecticide resistance in many populations leads to more difficulties for population management. To control movement of populations and apparitions of resistance carried by resistant migrant individuals, populations must be identified using genetic markers. Here, seven different ISSR markers have been tested as a tool for population discrimination and genetic variations among 19 DBM populations from Canada, USA, Brazil, Martinique Island, France, Romania, Austria, Uzbekistan, Egypt, Benin, South Africa, Réunion Island, Hong Kong, Laos, Japan and four localities in Australia were assessed. Two classification methods were tested and compared: a common method of genetic distance analyses and a novel method based on an advanced statistical method of the Artificial Neural Networks' family, the Self-Organizing Map (SOM). The 188 loci selected revealed a very high variability between populations with a total polymorphism of 100% and a global coefficient of gene differentiation estimated by the Nei's index (Gst) of 0.238. Nevertheless, the largest part of variability was expressed among individuals within populations (AMOVA: 73.71% and mean polymorphism of 94% within populations). Genetic differentiation among the DBM populations did not reflect geographical distances between them. The two classification methods have given excellent results with less than 1.3% of misclassified individuals. The origin of the high genetic differentiation and efficiency of the two classification methods are discussed.     

Nuclear and mitochondrial DNA reveals isolation of imperilled grey nurse shark populations (Carcharias taurus)

Loss of sharks and other upper-trophic marine predators has sparked worldwide concern for the stability of ocean ecosystems. The grey nurse (ragged-tooth or sand tiger) shark ( Carcharias taurus ) is Vulnerable on a global scale, Critically Endangered in Australia and presumed extinct in parts of its historical range. We used 193 muscle and fin samples collected from six extant populations to assess global mtDNA and microsatellite diversity and the degree of global population genetic structure. Control region mtDNA diversity was low in every population, and two populations (eastern Australia and Japan) contained only a single mtDNA haplotype. Genetic signatures of recent losses of genetic variation were not yet apparent at microsatellite loci, indicating that this low mtDNA variation is not a result of anthropogenic population declines. Population differentiation was substantial between each population pair except Brazil and South Africa, F _ST values ranged from 0.050 to 0.699 and 0.100 to 1.00 for microsatellite and mitochondrial data respectively. Bayesian analysis clearly partitioned individuals into five of the populations from which they were sampled. Our data imply a low frequency of immigrant exchange among each of these regions and we suggest that each be recognized as a distinct evolutionary significant unit. In contrast to pelagic species such as whale shark and white shark that may cross ocean basins and where cooperative international efforts are necessary for conservation, grey nurse shark, like many coastal species, need to be managed regionally.     

Biodemoraphy and genetics of the Berba of Benin

Genetic structure of the Berba of Benin was studied on the basis of biodemographic data and ABO, RH, MNS, KEL, JK, FY, ACP1, ADA, AK1, CA2, ESD, GLO1, G6PD, PGD, PGM1 (subtypes and thermostability), PGM2, PGP, SODA, HBα, HBβ, HBδ, BF, C3, and Hp gene frequencies. Comparisons were carried out with other populations of Benin and of sub-Sahara Africa. Correspondence analysis revealed genetic differentiation among the three main groups of populations who inhabit sub-Saharan Africa: Bushmen-Hottentots, Pygmies, and Negroes. The genetic differentiation of the Negroes in relation to their linguistic affiliation and geographic localization was evident. The first group included the populations belonging to the Bantoid subfamily of the Nigritic linguistic stock living in southern Africa; in the second subcluster the populations of central-eastern Africa were localized, and the third subcluster included the populations living in the West. © 1996 Wiley-Liss, Inc.     

Allozyme variability in an invasive drosophilid,Zaprionus indianus (Diptera: Drosophilidae): comparison of a recently introduced Brazilian population with Old World populations

Colonizing species often go through genetic bottlenecks when new territories are invaded. The South American continent has been recently colonized by a generalist African drosophilid, Zaprionus indianus, which has become an agricultural pest in Brazil in the last five years. In this paper we used allozyme electrophoresis to estimate levels of genetic differentiation of Z. indianus collected from sites 4 300 km apart in Brazil. We also compared the level of polymorphism of the Brazilian populations with that found in laboratory strains from Africa and Asia, to verify if a significant decrease in gene variability has taken place during the invasion process. The populations were polymorphic for three out of the 11 loci investigated. Genetic distances and F_ST indices among Brazilian populations were small and generally non significant, suggesting a colonization from one single propagule followed by a rapid demographic expansion. Ancestral and old populations from Africa and Asia were slightly more heterozygous than those from Brazil. Compared to other drosophilids, Z. indianus appears to be characterized by a low proportion (25%) of polymorphic loci. We suggest that the propagule introduced to Brazil had a sufficient size to carry almost all the polymorphism from the (unknown) origin population, although not the precise allelic frequencies.     

Assessment of the domestication state of ackee (Blighia sapida K.D. Koenig) in Benin based on AFLP and microsatellite markers

Ackee (Blighia sapida) is a native multipurpose species important for the livelihoods of the rural populations in Benin. Trees are found in natural forests or are managed by farmers in different traditional agroforestry systems. Genetic variation at amplified fragment length polymorphism (AFLP) markers, four nuclear microsatellites (nSSRs) and one chloroplast microsatellite (cpSSR) were investigated in 279 individuals from six wild and eight cultivated populations from Benin. The AFLP data revealed moderate levels of diversity of ackee in Benin (mean diversity values are proportion of polymorphic loci = 52.8% and Nei??s gene diversity = 0.157, for 375 AFLP fragments). The mean diversity values based on nSSR-markers are expected heterozygosity = 0.286, allelic richness = 2.77. Genetic variation of wild and cultivated populations did not differ markedly. AMOVA revealed that only 7.3 and 5.2% of the variation was partitioned among populations for nSSR- and AFLP-markers, respectively. A Mantel test based on these both marker-types revealed significant correlations between population pairwise geographic distance and genetic differentiation. Differentiation among cultivated populations was higher than among wild populations. The only polymorphic chloroplast microsatellite marker (ccmp7) showed three haplotypes. Cultivated populations from northeastern Benin were fixed on one haplotype which was not observed elsewhere indicating a different origin of these populations possibly from neighboring Nigeria. Farmer-led domestication had an impact on the spatial distribution of genetic variation but did not result in significant losses of diversity within populations. Measures to conserve genetic resources of ackee in each of the three main bioclimatic zones in Benin are proposed.     

Morphological variation and reproductive incompatibility of three coconut-mite-associated populations of predatory mites identified as Neoseiulus paspalivorus (Acari: Phytoseiidae)

Predatory mites identified as Neoseiulus paspalivorus DeLeon (Phytoseiidae) have been considered as agents for classical biological control of the coconut mite, Aceria guerreronis Keifer (Eriophyidae), in Africa and elsewhere. Preliminary identification of geographically distinct populations as belonging to the same species (N. paspalivorus) was based on their morphological similarity. However, laboratory studies recently conducted have shown large differences in feeding behaviors and biological characteristics among individuals collected from three geographic origins: Brazil (South America), Benin and Ghana (West Africa). As morphologically similar specimens do not necessarily belong to the same species, we evaluated under laboratory conditions, reproductive compatibility between the specimens from three geographic locations to ascertain their conspecificity. Morphological measurements were also made to determine whether there is a means of discriminating between them. Inter-population crosses showed complete reproductive isolation between the three geographic populations, but interpopulation discontinuities in morphometric characters were absent. These results indicate that the tested specimens are distinct biological entities despite morphological similarity. Further molecular genetic studies are therefore proposed, including screening for endosymbionts and assessment of genetic differentiation, to determine the cause of reproductive incompatibility and to clarify the taxonomic relationship between those populations.     

Genetic variation in central and peripheral populations of Excoecaria agallocha from Indo-West Pacific

Genetic diversity and differentiation were studied in Excoecaria agallocha L., a mangrove species growing on the coastlines of the Indo-West Pacific region. Twenty natural populations of E. agallocha were sampled from the Malay Peninsula (central population), and in Southern China, North Australia, Sri Lanka and Southern Japan (peripheral populations). Our results showed that central populations from Malay Peninsula possessed significantly higher genetic diversity than the peripheral ones (P < 0.05). Analysis of molecular variation (AMOVA) revealed that genetic variability was partitioned at 22.9% among regions, 23.6% among populations within regions, and 53.5% within populations. Genetic differentiation (G_ST = 0.300) among the six central populations was stronger than those from peripheral regions. Populations from North Australia clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Southern Japan, Southern China and Sri Lanka also clustered closely together, respectively. However, populations from Malay Peninsula did not cluster by region. The east coast populations of Malay Peninsula (including Pasir population) were more genetically similar to the populations from Southern China than those from the west coastline of Malay Peninsula. Our study suggests that ocean currents, land barriers, limited dispersal ability of seeds, and founder effect may play important roles in the distribution of genetic diversity in E. agallocha.     

Genetic diversity and maternal origin of Northeast African and South American donkey populations

To investigate the mtDNA variation and origin of maternal lineages in South American donkeys and to reassess the domestication of donkeys in northeast Africa, we analyzed sequences (489 bp of the D‐loop) from 323 domestic donkeys sampled from Peru, Brazil, Ethiopia and Egypt. Altogether, the 323 sequences displayed 53 different haplotypes (45 in Ethiopia, 14 in Egypt, eight in Peru and six in Brazil). Among the four populations, Egyptian donkeys possessed the highest haplotype diversity (0.910 ± 0.032), followed by Brazilian donkeys (0.879 ± 0.060). The Clade I haplotypes dominated in Peruvian donkeys (65%), whereas Clade II haplotypes dominated in Brazilian donkeys (67%). Estimates of F_ST values showed a high genetic differentiation between Peruvian and Brazilian donkey populations (F_ST = 0.4066), which could be explained by the complex introduction history of South American donkeys. Phylogeographic analysis indicates that northeast Africa could be the most probable domestication center for Clade I donkeys. Analysis of molecular variance confirmed a weak genetic structure in domestic donkey populations among four continents (Europe, Asia, Africa and South America).     

Microsatellite analysis of genetic diversity in African buffalo (Syncerus caffer) populations throughout Africa

Genetic diversity in nine African buffalo (Syncerus caffer) populations throughout Africa was analysed with 14 microsatellites to study the effects of rinderpest epidemics and habitat fragmentation during the 20th century. A gradient of declining expected heterozygosity was observed among populations in Save Valley Conservancy (Zimbabwe), and northern and southern Kruger National Park (South Africa). This was explained by a high mortality in northern Kruger National Park during the rinderpest pandemic at the end of the 19th century followed by recolonization from neighbouring populations, resulting in intermediate heterozygosity levels in northern Kruger National Park. In other populations expected heterozygosity was very high, indicating that rinderpest and recent habitat fragmentation had a limited effect on genetic diversity. From expected heterozygosity, estimates of long-term effective population size were derived. Migration rates among populations in eastern and southern Africa were very high, as shown by a weak isolation by distance and significant correlation in allele frequencies between populations. However, there were indications that dry habitats could limit migration. Genetic distances within buffalo in central Africa were relatively large, supporting their status as distinct subspecies. Finally, it was observed that the higher polymorphic microsatellites were less sensitive at detecting isolation by distance and differences in Ne, which may be a result of the high mutation pressure at these loci.     

Genetic diversity in Hemileia vastatrix based on RAPD markers

Random amplified polymorphic DNA (RAPD) was used to assess the genetic structure of Hemileia vastatrix populations. Forty-five rust isolates with different virulence spectra and from different hosts and geographical regions were analyzed. Out of 45 bands, generated with three RAPD primers, 35 (78%) were polymorphic and scored as molecular markers. Cluster analysis exhibits unstructured variability of this pathogen with regard to physiological race, geographical origin or host. The genotypic diversity (H') inferred from Shannon's index was higher than gene diversity (Ht), suggesting that diversity is distributed among clonal lineages. Estimates of gene diversity in Africa and Asia populations were higher in total (Ht) as compared to within population diversity (Hs). Genetic differentiation was considerable among coffee rust isolates from Africa (Gst = 0.865) and Asia (Gst = 0.768) but not among isolates from South America (Gst = 0.266). We concluded that genetic diversity in H. vastatrix was moderately low and that the genetic differentiation among populations shows that asexual reproduction is likely to play an important role in the population biology of this fungus. This should be taken into account for the development of breeding programs.     

Implications of isolation and low genetic diversity in peripheral populations of an amphi-Atlantic coral

Limited dispersal and connectivity in marine organisms can have negative fitness effects in populations that are small and isolated, but reduced genetic exchange may also promote the potential for local adaptation. Here, we compare the levels of genetic diversity and connectivity in the coral Montastraea cavernosa among both central and peripheral populations throughout its range in the Atlantic. Genetic data from one mitochondrial and two nuclear loci in 191 individuals show that M. cavernosa is subdivided into three genetically distinct regions in the Atlantic: Caribbean-North Atlantic, Western South Atlantic (Brazil) and Eastern Tropical Atlantic (West Africa). Within each region, populations have similar allele frequencies and levels of genetic diversity; indeed, no significant differentiation was found between populations separated by as much as 3000 km, suggesting that this coral species has the ability to disperse over large distances. Gene flow within regions does not, however, translate into connectivity across the entire Atlantic. Instead, substantial differences in allele frequencies across regions suggest that genetic exchange is infrequent between the Caribbean, Brazil and West Africa. Furthermore, markedly lower levels of genetic diversity are observed in the Brazilian and West African populations. Genetic diversity and connectivity may contribute to the resilience of a coral population to disturbance. Isolated peripheral populations may be more vulnerable to human impacts, disease or climate change relative to those in the genetically diverse Caribbean-North Atlantic region.     

Low genetic differentiation among widely separated populations of the pearl oyster Pinctada fucata as revealed by AFLP

Genetic variation within and among five populations of the pearl oyster Pinctada fucata, from China (Daya Bay, Sanya Bay and Beibu Bay), Japan (Mie Prefecture) and Australia (Port Stephens) was studied using AFLP. Three primer pairs generated 184 loci among which 91.8-97.3% is polymorphic. An overall genetic diversity of 0.38 among populations and an average of 0.37 within populations (ranging from 0.35 in Japanese population to 0.39 in Beibu Bay population) were observed. Genetic differentiation among the five populations is low but significant as indicated by pairwise G_ST (0.0079-0.0404). AMOVA further shows that differentiation is significant among the five populations but is not significant at a broader geographical scale, among the three groups of Chinese, Japanese and Australian populations or among the two groups of Australian and north Pacific populations. The low level of genetic differentiation indicated that P. fucata populations in the west Pacific are genetically linked. Among the five populations, the Australian one is more differentiated from the others, based on both pairwise AMOVA and G_ST analyses, and is genetically isolated by distance as indicated by Mantel test. However, genetic differences among the three Chinese populations are not correlated with the geographic distances, suggesting that Hainan Island and Leizhou Peninsula may act as barriers blocking gene flow.     

Out of Africa: the slow train to australasia

We used mitochondrial DNA (mtDNA) sequences to test biogeographic hypotheses for Patiriella exigua (Asterinidae), one of the world's most widespread coastal sea stars. This small intertidal species has an entirely benthic life history and yet occurs in southern temperate waters of the Atlantic, Indian, and Pacific oceans. Despite its abundance around southern Africa, southeastern Australia, and several oceanic islands, P. exigua is absent from the shores of Western Australia, New Zealand, and South America. Phylogenetic analysis of mtDNA sequences (cytochrome oxidase I, control region) indicates that South Africa houses an assemblage of P. exigua that is not monophyletic (P = 0.04), whereas Australian and Lord Howe Island specimens form an interior monophyletic group. The placement of the root in Africa and small genetic divergences between eastern African and Australian haplotypes strongly suggest Pleistocene dispersal eastward across the Indian Ocean. Dispersal was probably achieved by rafting on wood or macroalgae, which was facilitated by the West Wind Drift. Genetic data also support Pleistocene colonization of oceanic islands (Lord Howe Island, Amsterdam Island, St. Helena). Although many biogeographers have speculated about the role of long-distance rafting, this study is one of the first to provide convincing evidence. The marked phylogeographic structure evident across small geographic scales in Australia and South Africa indicates that gene flow among populations may be generally insufficient to prevent the local evolution of monophyly. We suggest that P. exigua may rely on passive mechanisms of dispersal.     

Genetic Variation in TLR Genes in Ugandan and South African Populations and Comparison with HapMap Data

Genetic epidemiological studies of complex diseases often rely on data from the International HapMap Consortium for identification of single nucleotide polymorphisms (SNPs), particularly those that tag haplotypes. However, little is known about the relevance of the African populations used to collect HapMap data for study populations conducted elsewhere in Africa. Toll-like receptor (TLR) genes play a key role in susceptibility to various infectious diseases, including tuberculosis. We conducted full-exon sequencing in samples obtained from Uganda (n = 48) and South Africa (n = 48), in four genes in the TLR pathway: TLR2, TLR4, TLR6, and TIRAP. We identified one novel TIRAP SNP (with minor allele frequency [MAF] 3.2%) and a novel TLR6 SNP (MAF 8%) in the Ugandan population, and a TLR6 SNP that is unique to the South African population (MAF 14%). These SNPs were also not present in the 1000 Genomes data. Genotype and haplotype frequencies and linkage disequilibrium patterns in Uganda and South Africa were similar to African populations in the HapMap datasets. Multidimensional scaling analysis of polymorphisms in all four genes suggested broad overlap of all of the examined African populations. Based on these data, we propose that there is enough similarity among African populations represented in the HapMap database to justify initial SNP selection for genetic epidemiological studies in Uganda and South Africa. We also discovered three novel polymorphisms that appear to be population-specific and would only be detected by sequencing efforts.     

DNA bar-coding reveals source and patterns of <Emphasis Type="Italic">Thaumastocoris peregrinus</Emphasis> invasions in South Africa and South America

Thaumastocoris peregrinus is a recently introduced invertebrate pest of non-native Eucalyptus plantations in the Southern Hemisphere. It was first reported from South Africa in 2003 and in Argentina in 2005. Since then, populations have grown explosively and it has attained an almost ubiquitous distribution over several regions in South Africa on 26 Eucalyptus species. Here we address three key questions regarding this invasion, namely whether only one species has been introduced, whether there were single or multiple introductions into South Africa and South America and what the source of the introduction might have been. To answer these questions, bar-coding using mitochondrial DNA (COI) sequence diversity was used to characterise the populations of this insect from Australia, Argentina, Brazil, South Africa and Uruguay. Analyses revealed three cryptic species in Australia, of which only T. peregrinus is represented in South Africa and South America. Thaumastocoris peregrinus populations contained eight haplotypes, with a pairwise nucleotide distance of 0.2–0.9% from seventeen locations in Australia. Three of these haplotypes are shared with populations in South America and South Africa, but the latter regions do not share haplotypes. These data, together with the current distribution of the haplotypes and the known direction of original spread in these regions, suggest that at least three distinct introductions of the insect occurred in South Africa and South America before 2005. The two most common haplotypes in Sydney, one of which was also found in Brisbane, are shared with the non-native regions. Sydney populations of T. peregrinus, which have regularly reached outbreak levels in recent years, might thus have served as source of these three distinct introductions into other regions of the Southern Hemisphere.     

基于线粒体COI基因的桔小实蝇种群遗传分化研究

【目的】推测桔小实蝇Bactrocera dorsalis在中国的扩散路径和新发生地区的入侵来源。【方法】本研究测序获得来自中国、泰国、日本、老挝、孟加拉国和美国等地31个种群的192头桔小实蝇个体的COI序列（1 496 bp,占COI基因全长97.3%）,并以软件DnaSP 5.0, MEGA 6.0和Arlequin 3.5等完成各种群的遗传多样性、种群间的遗传分化以及单倍型分析。【结果】所测31个桔小实蝇种群总体表现出较高水平的核苷酸多样性（0.00663）和高水平的单倍型多样性（0.98069）。以F-统计法度量种群间遗传分化程度, 结果显示中国桔小实蝇地理种群间遗传分化较弱, 中国种群与泰国、日本、老挝、孟加拉国、美国种群间的遗传分化程度不同, 中国种群与美国种群及日本种群的遗传分化最大。而Mantel检验发现,中国、泰国、日本、老挝、孟加拉国和美国种群间的遗传分化与空间距离有关（R=0.670, P<0.0001）, 中国种群间的遗传分化不是地理隔离所造成的（R=0.038, P=0.534）。中国种群与泰国、日本、老挝、孟加拉国和美国种群间不存在共享单倍型。根据种群系统发育树,可将中国原发生地区种群划分为西南、东南两大分支。中性检验和错配分析结果均表明桔小实蝇曾存在大规模的扩张。【结论】桔小实蝇以东南地区和西南地区为源头向中国内陆扩散,其中广东、福建、广西和贵州种群为中国内陆种群较为有影响力的源头。根据遗传多样性、遗传分化、单倍型分析,推测新发生地区桔小实蝇的来源, 例如安徽合肥桔小实蝇种群主要来源于福建长乐、广东珠海和上海。     

Frequency and origins of hemoglobin S mutation in African-derived Brazilian populations

Africans arrived in Brazil as slaves in great numbers, mainly after 1550. Before the abolition of slavery in Brazil in 1888, many communities, called quilombos, were formed by runaway or abandoned African slaves. These communities are presently referred to as remnants of quilombos, and many are still partially genetically isolated. These remnants can be regarded as relicts of the original African genetic contribution to the Brazilian population. In this study we assessed frequencies and probable geographic origins of hemoglobin S (HBB*S) mutations in remnants of quilombo populations in the Ribeira River valley, S?o Paulo, Brazil, to reconstruct the history of African-derived populations in the region. We screened for HBB*S mutations in 11 quilombo populations (1,058 samples) and found HBB*S carrier frequencies that ranged from 0% to 14%. We analyzed beta-globin gene cluster haplotypes linked to the HBB*S mutation in 86 chromosomes and found the four known African haplotypes: 70 (81.4%) Bantu (Central Africa Republic), 7 (8.1%) Benin, 7 (8.1%) Senegal, and 2 (2.3%) Cameroon haplotypes. One sickle cell homozygote was Bantu/Bantu and two homozygotes had Bantu/Benin combinations. The high frequency of the sickle cell trait and the diversity of HBB*S linked haplotypes indicate that Brazilian remnants of quilombos are interesting repositories of genetic diversity present in the ancestral African populations.     

High microsatellite diversity and differential structuring among populations of the introduced common brushtail possum, Trichosurus vulpecula, in New Zealand

An understanding of genetic variation and structure of pest populations has the potential to improve the efficiency of measures to control them. Genetic analysis was undertaken at five microsatellite loci in four native Australian and 14 introduced New Zealand populations of the common brushtail possum Trichosurus vulpecula in order to document these parameters. Genetic variation in New Zealand populations, and phylogenetic relationships among Australian and New Zealand populations, were largely predicted by the recorded introduction history. Populations on the two main islands of New Zealand had only slightly lower genetic diversity than did Australian populations, except that allelic richness on the South Is. was significantly lower. Diversity was higher in North Is. than in South Is. populations (although not significantly so) and mainland New Zealand populations as a group were significantly more diverse than offshore islands that represented secondary population size bottlenecks. In phylogenetic analyses South Is. and offshore island populations grouped with Tasmania, while North Is. populations grouped either with mainland Australia or were intermediate between the two Australian sources. This scheme was supported by admixture coefficients showing that North and South Is./offshore island populations were largely mainland Australian and Tasmanian in origin, respectively. Population structure differed markedly between the North and South Islands: populations were typically more genetically differentiated on the former than the latter, which also showed significant isolation-by-distance. Substantial linkage disequilibrium in most sampled New Zealand but no Australian population between microsatellite loci Tv16 and Tv27 suggests they may be physically linked.     

Patterns of genetic differentiation in two annual bromegrasses,Bromus lanceolatus andB. hordeaceus (Poaceae)

Infraspecific genetic differentiation was analysed in two tetraploid annual bromegrasses,Bromus lanceolatus (from N Africa) andB. hordeaceus (from N Africa and France). Genetic analysis of populations was based on allozyme polymorphisms at 17 loci. Different fixed heterozygous phenotypes were scored in both species, according to their allopolyploid origin. In N Africa, more variation occurred among populations ofB. lanceolatus than ofB. hordeaceus. The variation was not randomly distributed among populations of both species. InB. lanceolatus, differentiation was correlated with climatic variables rather than with geographic distance between populations. Higher correlation of genetic differentiation with geographic distance occurred inB. hordeaceus, particularly at large geographic scale, between French and N African populations. Within each region, the populations appeared weakly genetically differentiated, even when belonging to different subspecies.     

An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence-tagged microsatellites (SSRs) and AFLPs

Genetic diversity in 31 individuals from 14 coconut populations across the entire geographic range (2–3 individuals per population) was assessed using sequence-tagged microsatellites (or simple sequence repeats, SSRs) and amplified fragment length polymorphism (AFLP). From the 39 SSR primer sets tested, only two gave patterns that could not be scored and used in the data analysis. The remainder included five SSRs that gave double-locus profiles in which one locus could still be scored separately. The 37 SSRs revealed between 2 and 16 alleles per locus and a total of 339 alleles in the 14 populations. Gene diversity (D = 1-Σp_i ²) ranged from 0.47 to 0.90. Two of the four Dwarf populations were homozygous at all 37 loci, which is consistent with their autogamous (self-fertilising) reproduction. One Dwarf population was heterozygous at one locus but the other (Niu Leka Dwarf), which is known to be cross-pollinating, showed high levels of heterozygosity. Generally, diversity was higher in populations from the South Pacific and South East Asia. Three SSR loci (CNZ46, CN2A5, CN11E6) gave distinct genotypes for all but two populations. The East African populations had higher heterozygosities than those from West Africa, and the populations from Tonga and Fiji generally had distinct alleles from those of the South Pacific. AFLP analysis with 12 primer combinations gave a total of 1106 bands, of which 303 were polymorphic (27%). Similarity matrices were constructed from the two data sets using the proportion of shared alleles for SSRs and a Jaccard coefficient for AFLPs. In each case cluster and principal co-ordinates analyses were performed, with the resultant dendrograms and plots revealing similar relationships among the populations for both approaches. There was generally a good separation of populations, and phenetic relationships were in agreement with those previously shown by RFLPs. The use of SSRs and AFLPs in genetic-diversity analysis for the establishment of germplasm collections is discussed. Received: 27 October 1998 / Accepted: 31 March 1999