Genetic Diversity and Geographical Differentiation of <Emphasis Type="Italic">Desmodium triflorum</Emphasis> (L.) DC. in South China Revealed by AFLP Markers

High levels of genetic variation enable species to adapt to changing environments and provide plant breeders with the raw materials necessary for artificial selection. In the present study, six AFLP primer pairs were used to assess the genetic diversity of Desmodium triflorum (L.) DC. from 12 populations in South China. A high percentage of polymorphic loci (P = 76.16%) and high total gene diversity (H _T = 0.310) were found, indicating that the genetic diversity of D. triflorum is high at the species level. Genetic diversity was also relatively high at the population level (P = 55.85%, H _e = 0.230). The coefficient of gene differentiation among populations (G _ST) was 0.255, indicating that while most genetic diversity resided within populations, there was also considerable differentiation among populations. AMOVA also indicated 24.29% of the total variation to be partitioned among populations (Φ_ST = 0.243). UPGMA clustering analysis based on genetic distances showed that the 12 populations could be separated into three subgroups: an eastern, a western, and a central-southern subgroup. However, a Mantel test revealed no significant correlation (r = 0.286, p = 0.983) between the geographical distances and genetic distances separating these populations; mountain barriers to gene flow and human disturbance may have confounded these correlations. The present study has provided some fundamental genetic data that will be of use in the exploitation of D. triflorum.     

Landscape genetic structure of <Emphasis Type="Italic">Betula maximowicziana</Emphasis> in the Chichibu mountain range,central Japan

We evaluated the genetic structure of 16 Betula maximowicziana populations in the Chichibu mountain range, central Japan, located within a 25-km radius; all but two populations were at altitudes of 1,100–1,400 m. The results indicate the effects of geographic topology on the landscape genetic structure of the populations and should facilitate the development of local-scale strategies to conserve and manage them. Analyses involving 11 nuclear simple sequence repeat loci showed that most populations had similar intrapopulation genetic diversity parameters. Population differentiation (F _ST = 0.021, G′_ST = 0.033) parameters for the populations examined were low but were relatively high compared to those obtained in a previous study covering populations in a much larger area with a radius of approximately 1,000 km (F _ST = 0.062, G′_ST = 0.102). Three populations (Iriyama, Kanayamasawa, and Nishizawa) were differentiated from the other populations by Monmonier’s and spatial analysis of molecular variance algorithms or by STRUCTURE analysis. Since a high mountain ridge (nearly 2,000 m) separates the Kanayamasawa and Nishizawa populations from the other 14 populations and the Kanayamasawa and Nishizawa populations are themselves separated by another mountain ridge, the genetic structure appears to be partly due to mountain ridges acting as genetic barriers and restricting gene flow. However, the Iriyama population is genetically different but not separated by any clear geographic barrier. These results show that the landscape genetic structure is complex in the mountain range and we need to pay attention, within landscape genetic studies and conservation programs, to geographic barriers and local population differentiation.     

Genetic diversity and population differentiation in the endangered Siberian flying squirrel (<Emphasis Type="Italic">Pteromys volans</Emphasis>) in a fragmented landscape

Siberian flying squirrel (Pteromys volans) has declined in Finland and it is considered an endangered species. We studied microsatellite variation in four flying squirrel populations in a fragmented landscape in Finland to determine the amount of gene flow and genetic diversity in the populations. Demographic data from these areas suggest that the populations are declining. All the populations are significantly differentiated (F _ST = 0.23). The most notable result is the high degree of differentiation between two adjacent populations (F _ST = 0.11) and low genetic variability (number of alleles 3.0) in one of the populations. These findings suggest problems in dispersal and possible fragmentation effects in the landscape where only 10–20% of habitat favorable for the flying squirrel is left. Conservation ensuring dispersal should be urgently considered. Future studies should concentrate on the modeling of the population viability and on the effects of inbreeding in these small populations. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Maintenance of genetic diversity in Cordia africana Lam., a declining forest tree species in Ethiopia

We assessed genetic variation in a total of 22 populations of the tree species Cordia africana Lam. in Ethiopia and analyzed the country-wide impact of population history, forest disturbance and alteration of land use on extant intraspecific diversity. Amplified Fragment Length Polymorphisms (AFLPs) and chloroplast microsatellite markers were investigated. The analyses of the AFLP data revealed high diversity in all investigated populations: the percentage of polymorphic loci (PPL) ranged from 62.2% to 92.2% and Nei's gene diversity from 0.220 to 0.320 within the populations. The mean PPL and the mean diversity within populations were 85.7% and 0.287, respectively. The analysis of molecular variance revealed a moderate level of differentiation (Φ_ST = 0.07, p < 0.001) among the populations. The Mantel test proved a significant but low correlation (r = 0.31, p < 0.001) between the geographic distance and the genetic differentiation matrices. Only three different cpDNA haplotypes were observed; no more than two haplotypes were found in any population. The dominant haplotype with an overall frequency of 81% was observed in all populations. The level of differentiation among the populations was comparatively low at chloroplast DNA (G _ST = 0.18, R _ST, N _ST = 0.22). The observed patterns and levels of genetic variation within and among the populations indicate that efficient gene flow via pollen and seed is likely to be the main factor contributing to the maintenance of genetic diversity in natural and disturbed conditions.     

Population genetic structure of the endangered and endemic medicinal plant <Emphasis Type="Italic">Commiphora</Emphasis><Emphasis Type="Italic">wightii</Emphasis>

Commiphora wightii is a medicinally important endangered species endemic to the Thar Desert of Rajasthan, India and adjoining areas of Pakistan. The populations of this species are declining sharply because of its extensive use as a natural herb. Random amplified polymorphic DNA analysis was conducted to find the genetic variation among 7 populations of C. wightii. Of the 100 random primers screened, 44 primers yielded 220 loci. Statistical analysis indicated low genetic diversity (H _pop = 0.0958; I = 0.1498; mean polymorphic loci = 14.28%), and high genetic differentiation among the populations (G _ST = 0.3990; AMOVA Φ _ST of 0.3390; Bayesian θ ^(II) = 0.3002). The low genetic diversity may be due to geographic isolation and restricted gene flow (N _m = 0.7533) between the fragmented populations. Unsustainable utilization of the plant has fragmented the population continuum which served the purpose of genetic exchange between populations. Mantel’s test was performed which revealed a highly significant positive correlation between genetic and geographic distance (r ² = 0.614, P = 0.023) among the populations studied. Low variation can also be attributed to poor seed setting and the slow growth pattern of the species, which is also an apomict. In UPGMA dendrogram the Commiphora wightii samples were divided into two major and one minor cluster. These findings can serve as a guide to preserving the genetic resources of this medicinal plant species.     

Wild genetic diversity preservation in a small-sized first generation breeding population of <Emphasis Type="Italic">Allanblackia floribunda</Emphasis> (Clusiaceae)

Founder group size is of prime importance in tree breeding programs. We determined whether sampling 20-plus trees for breeding in Allanblackia floribunda, a tropical forest tree species that has been recently enrolled in tree improvement program for fruit and seed production, would affect neutral genetic diversity and inbreeding level in both breeding and production populations. Using eight informative microsatellite loci, we: (a) assessed the nuclear genetic diversity of ten natural populations, and of the breeding population in the humid forest zone of Cameroon; (b) investigated temporal effective-size fluctuations in A. floribunda natural populations, with a view to identifying the role of past demographic events in the genetic structure of the studied species; and (c) tested the hypothesis that genetic diversity in a founder group of 20 individuals is not different from that existing in the wild. The eight loci were variable. High levels of genetic diversity (A = 4.96; H _E = 0.59) and moderate differentiation (R _ST = 0.061) were found within and among populations in wild stands. High genetic distances existed between populations ( \textaverage chord distance = 0.\text2769 ±0.00\text554 ) \left( {{\text{average chord distance}} = 0.{\text{2769}} \pm 0.00{\text{554}}} \right) . Eight of the ten surveyed populations showed signs of deviation from mutation-drift equilibrium, suggesting Pleistocene population bottlenecks and fluctuations in effective population size. Mantel tests did not reveal any relationships between genetic and geographic distances. A neighbor-joining dendrogram showed a population structure that could be explained by historical factors. The hypothesis tested has been accepted. However, a slight increase in inbreeding was observed in the breeding population.     

Contrasting population genetic structure and gene flow between <Emphasis Type="Italic">Oryza rufipogon</Emphasis> and <Emphasis Type="Italic">Oryza nivara</Emphasis>

The cross compatible wild relatives of crops have furnished valuable genes for crop improvement. Understanding the genetics of these wild species may enhance their further use in breeding. In this study, sequence variation of the nuclear Lhs1 gene was used to investigate the population genetic structure and gene flow of Oryza rufipogon and O. nivara, two wild species most closely related to O. sativa. The two species diverge markedly in life history and mating system, with O. rufipogon being perennial and outcrossing and O. nivara being annual and predominantly inbreeding. Based on sequence data from 105 plants representing 11 wild populations covering the entire geographic range of these wild species, we detected significantly higher nucleotide variation in O. rufipogon than in O. nivara at both the population and species levels. At the population level the diversity in O. rufipogon (Hd = 0.712; θ _sil = 0.0017) is 2–3 folds higher than that in O. nivara (Hd = 0.306; θ _sil = 0.0005). AMOVA partitioning indicated that genetic differentiation among O. nivara populations (78.2%) was much higher than that among O. rufipogon populations (52.3%). The different level of genetic diversity and contrasting population genetic structure between O. rufipogon and O. nivara might be explained by their distinct life histories and mating systems. Our simulation using IM models demonstrated significant gene flow from O. nivara to O. rufipogon, indicating a directional introgression from the annual and selfing species into the perennial and outcrossing species. The ongoing introgression has played an important role in shaping current patterns of genetic diversity of these two wild species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Conservation genetics of the endangered endemic Sambucus palmensis Link (Sambucaceae) from the Canary Islands

Five polymorphic microsatellites (simple sequence repeat; SSR) markers were used to estimate the levels of genetic variation within and among natural populations from different islands of the endangered endemic from the Canary Islands Sambucus palmensis Link (Sambucaceae). Genetic data were used to infer potential evolutionary processes that could have led to present genetic differentiation among islands. The levels of genetic variability of S. palmensis were considerably high; proportion of polymorphic loci (P = 100%), mean number of alleles per locus (A = 6.8), average expected heterozygosity (He = 0.499). In spite of its small population size and endemic character, 58 different multilocus genotypes were detected within the 165 individuals analyzed. All samples located in different islands always presented different multilocus genotypes. Principal Coordinates Analysis, genetic differentiation analysis (F _ST and G _ST ′) and Bayesian Cluster Analysis revealed significant genetic differences among populations located in different islands. However, this genetic differentiation was not recorded among Tenerife and La Gomera populations, possibly revealing the uncontrolled transfer of material between both islands. AMOVA analysis attributed 77% of the variance to differences within populations, whereas 8% was distributed between islands. The levels of genetic differentiation observed among populations, and the genetic diversity distribution within populations in S. palmensis, indicate that management should aim to conserve as many of the small populations as possible. Concentrating conservation efforts only on the few large populations would result in the likelihood of loss of genetic variability for the species.     

Mitochondrial DNA reveals low population differentiation in elongate loach, <Emphasis Type="Italic">Leptobotia elongata</Emphasis> (Bleeker): implications for conservation

Elongate loach (Leptobotia elongata (Bleeker)), an endemic fish species to China, is a famous ornamental freshwater fish. Here, a comparative study of mtDNA control region (D-loop) (835 bp) sequences was performed to analyze its wild population structure and evaluate the genetic diversity for 110 individuals from five locations in the upper reaches of the Yangtze River, China. A total of 49 polymorphic sites and 45 haplotypes yielded high haplotype diversity (h = 0.952), but low nucleotide diversity (π = 0.00454) as that of many fish species. Sequence divergences between haplotypes ranged from 0.0033 ± 0.0011 to 0.0050 ± 0.0012 in intra-groups, and from 0.0037 ± 0.0.0011 to 0.0050 ± 0.0012 between groups. Significant values of Tajima’s D (−1.86383, P < 0.01) and Fu’s F _S (−25.93, P < 0.01), together with uni-modal mismatch distribution, indicated a recent genetic bottleneck or population expansion of the species. Analysis of molecular variance (AMOVA) indicated a small amount of differentiation among groups (1.7%); most of the total variation occurred within groups (98.3%). Also, there was no significant population structure (F _ST = 0.017, P > 0.05), and estimates of gene flows among groups were extremely high (Nm = 28.88), suggesting low genetic divergence between populations in the species. The lack of genetic differentiation among groups is most likely due to the combined gene flow from the downstream movement of eggs and larvae with currents and the upstream or downstream migration of adults throughout the distribution. These groups of L. elongata distributed in upper reaches of the Yangtze River should be considered as a single management unit.     

An AFLP-based survey of genetic diversity and relationships of major farmed cultivars and geographically isolated wild populations of <Emphasis Type="Italic">Saccharina japonica</Emphasis> (Phaeophyta) along the northwest coasts of the Pacific

The genetic diversity and relationships of six representative cultivars and six geographically isolated wild populations of Saccharina japonica along the northwest coasts of the Pacific Ocean were investigated using AFLP markers. A total of 547 bands were generated across all samples by ten primer combinations. At the cultivar or population level, the percentage of polymorphic loci (P), gene diversity (H), and Shannon’s information index (I) was highest in Dalian population (P 59.05%; H 0.2057; I 0.3062) and lowest in Lianjiang cultivar (P 9.87%; H 0.0331; I 0.0497). At the species level, P, H, and I were 85.01%, 0.1948, and 0.3096, respectively. Unique bands were detected in all the six wild populations, with Dalian being the most. In comparison, only Yanza cultivar possessed one unique band. The G _ST value was 0.6226 and the gene flow (N _m ) was 0.1515, indicating strong genetic differentiation among cultivars and populations. Two UMPGA dendrograms were constructed based on the Dice similarity coefficients among individuals and on genetic distances among cultivars and populations, which generally revealed three major clades corresponding to three countries. Analysis of molecular variance revealed that a larger proportion (60.21%) of the total genetic variation was attributable to differences among cultivars and populations. The Mantel test suggested that genetic differentiation was positively correlated with geographic distance (r = 0.7962, P = 0.011) in the six wild populations, agreeing with the isolation by distance model. On the whole, low to moderate genetic diversity within cultivars and populations (except Dalian population) and high genetic differentiation among cultivars and populations were detected.     

High levels of genetic divergence and inbreeding in populations of cupuassu (Theobroma grandiflorum)

Theobroma grandiflorum (cupuassu) is an important fruit tree native to the Brazilian Amazon. Establishing the genetic diversity and structure of populations is critical to define long-term strategies for cupuassu conservation presently threatened by rapid deforestation. Three natural populations collected at the putative center of diversity, three groups of accessions established at a germplasm collection, and one derived from commercial plantings were analyzed. The genetic diversity was assessed using 21 polymorphic microsatellite loci originally developed for Theobroma cacao, disclosing a total of 113 alleles. The estimated genetic diversity parameters averaged over cupuassu populations (A = 3.53 alleles per locus; H _e = 0.426; H _o = 0.346) were lower than the values reported for other Neotropical tree species. The three natural populations presented a positive and significant fixation index (f), ranging from 0.133 to 0.234. Cupuassu apparently adhered to a general pattern of genetic diversity structure of some Neotropical tree species occurring at low densities, with a low intrapopulation genetic diversity and important levels of endogamy, possibly due to biparental inbreeding derived from the presence of spatial genetic structure in the populations. A high level of genetic divergence was detected among the natural populations (θ _p = 0.301), a strong differentiation caused by limited gene flow, and suggesting that human interference in spreading and/or stimulating plantings might have had a smaller effect than expected. The approximate location of the T. grandiflorum center of diversity could not be confirmed by analyzing natural populations from the putative region.     

Population genetics and fitness in fragmented populations of the dioecious and endangered <Emphasis Type="Italic">Silene otites</Emphasis> (Caryophyllaceae)

Population fragmentation is often correlated with loss of genetic diversity and reduced fitness. Obligate out-crossing (dioecy) is expected to enhance genetic diversity, reduce genetic differentiation, and avoid inbreeding depression through frequent gene flow. However, in highly fragmented populations dioecy has only diminishing effects upon genetic structure as pollination limitations (e.g. flight distance of pollinators) most often restrict inter-population gene flow in insect pollinated species. In fragmented dry grasslands in northeastern Germany, we analysed genetic structure, fitness, and habitat quality of the endangered dioecious Silene otites (Caryophyllaceae). Using AFLP markers, a high level of differentiation among ten populations was found (F _st = 0.36), while the intra-population genetic diversities (H _E = 0.165–0.240) were similar as compared to hermaphroditic species. There was neither a correlation between geographic and genetic distance nor between genetic diversity and population size, which indicates reduced gene flow among populations and random genetic drift. Plant size was positively correlated with genetic diversity. Seed set and number of juveniles were positively related to population size. Higher total coverage resulted in reduced plant fitness, and the number of juveniles was negatively correlated to cryptogam cover. Additionally, we found a sex ratio bias towards more male plants in larger populations. Overall, our results indicate that on a regional geographic scale dioecy does not necessarily prevent genetic erosion in the case of habitat fragmentation, especially in the absence of long distance seed and pollen dispersal capacity.     

Population structure and conservation genetics of the Oregon spotted frog, <Emphasis Type="Italic">Rana pretiosa</Emphasis>

The Oregon spotted frog (Rana pretiosa) is one of the most threatened amphibians in the Pacific Northwest. Here we analyzed data from 13 microsatellite loci and 298 bp of mitochondrial DNA in frogs collected from 23 of the remaining R. pretiosa populations in order to (1) assess levels of genetic diversity within populations of R. pretiosa, (2) identify the major genetic groups in the species, (3) estimate levels of genetic differentiation and gene flow among populations within each major group, and (4) compare the pattern of differentiation among R. pretiosa populations with that among populations of R. cascadae, a non-endangered congener that also occurs in Oregon and Washington. There is a strong, hierarchical genetic structure in R. pretiosa. That structure includes six major genetic groups, one of which is represented by a single remaining population. R. pretiosa populations have low genetic diversity (average H _e = 0.31) compared to R. cascadae (average H _e = 0.54) and to other ranid frogs. Genetic subdivision among populations is much higher in R. pretiosa than in R. cascadae, particularly over the largest geographic distances (hundreds of kilometers). A joint analysis of migration rates among populations and of effective sizes within populations (using MIGRATE) suggests that both species have extremely low migration rates, and that R. pretiosa have slightly smaller effective sizes. However, the slight difference in effective sizes between species appears insufficient to explain the large difference in genetic diversity and in large-scale genetic structure. We therefore hypothesize that low connectivity among the more widely-spaced R. pretiosa populations (owing to their patchier habitat), is the main cause of their lower genetic diversity and higher among-population differentiation. Conservation recommendations for R. pretiosa include maintaining habitat connectivity to facilitate gene flow among populations that are still potentially connected, and either expanding habitat or founding additional ‘backup’ populations to maintain diversity in the isolated populations. We recommend that special consideration be given to conservation of the Camas Prairie population in Northern Oregon. It is the most geographically isolated population, has the lowest genetic diversity (H _e = 0.14) and appears to be the only remaining representative of a major genetic group that is now almost extinct. Finally, because the six major groups within R. pretiosa are strongly differentiated, occupy different habitat types, and are geographically separate, they should be recognized as evolutionarily significant units for purposes of conservation planning.     

Genetic differences between continuous and disjunct populations: some insights from sal (<Emphasis Type="Italic">Shorea robusta</Emphasis> Roxb.) in Nepal

Sal (Shorea robusta Gaertn., Dipterocarpaceae) is a wind-pollinated tropical tree species found in southern Asia. We investigated the genetic diversity and structure at four microsatellites of 15 populations comprising continuous-peripheral and disjunct-peripheral populations in Nepal. Estimates of genetic diversity (N _A = 8.98, H _O = 0.62, H _E = 0.69) were similar when compared with those of other tropical tree species. A higher level of genetic diversity was observed in continuous-peripheral populations (N _A = 9.61, H _O = 0.67, H _E = 0.72) as compared to disjunct-peripheral (N _A = 8.04, H _O = 0.55, H _E = 0.64). Population differentiation was higher among disjunct-peripheral populations (F _ST = 0.043) than among continuous peripherals (F _ST = 0.012). There was a significant association between gene flow distances and genetic differentiation (r ² = 0.128, P ≤ 0.007). No spatial arrangement of populations according to their geographical locations was found. Based on observed genetic diversity protection of some populations in continuous-peripheral range are suggested for the sustainable conservation of genetic resources of the species while protection of some disjunct-peripheral populations are also recommended for conserving rare alleles.     

The effects of Quaternary glaciations in Patagonia as evidenced by chloroplast DNA phylogeography of Southern beech Nothofagus obliqua

Climatic oscillations during the Quaternary strongly affected the distribution of warm-temperate tree species, which experienced local restrictions into ice-free areas and posterior expansions. To evaluate the impact of these range movements on the genetic structure of populations, we performed a phylogeographical analysis of the species Nothofagus obliqua with chloroplast DNA markers. A total of 27 populations covering the whole natural distribution range were analyzed using polymerase chain reaction-restriction fragment length polymorphism. Diversity (h _T, h _S), allelic richness (r _g), and differentiation among populations for unordered (G _ST) and ordered alleles (N _ST) were calculated. The relationships among haplotypes were evaluated by the construction of a minimum spanning network. The spatial distribution of the genetic variation was analyzed through a Mantel test and with a nested analysis of molecular variance to differentiate between geographic regions. The screening of 11 non-coding regions allowed the identification of 14 haplotypes. A high genetic differentiation was detected (N _ST = 0.875 and G _ST = 0.824) with the existence of phylogeographic structure (p < 0.05). The distribution of the genetic variation was partially explained by the topography of the region when the populations were divided longitudinally into Coastal Mountains, Central Valley, and Andes Mountains (ϕ _RT = 0.093, p = 0.001). In agreement with pollen records, our results support the hypothesis of Coastal refuges since the region harbors high diversity together with older and private haplotypes. Long-lasting persistence of some Coastal populations without contribution to re-colonization is proposed. Additional refuges are also postulated along the Andes and Longitudinal Valley. Survival in multiple glacial refuges is discussed together with the possible migratory routes.     

Genetic variability and structure of the remnant natural populations of <Emphasis Type="Italic">Cedrus libani</Emphasis> (Pinaceae) of Lebanon

Cedrus libani of Lebanon is a valuable natural resource and the dominant species in its natural ecosystem. Intense and diverse anthropogenic pressures over historical times raised concerns about its genetic vigor and continued survival. Our investigation of the genetic diversity included samples from all remnant natural populations. Assessment of the genetic diversity using random amplified polymorphic DNA markers revealed the persistence of considerable variation distributed within populations with low population differentiation corroborated by Bayesian and analysis of molecular variance estimates (G _ST = 0.07, Φ _ST = 0.09). Individual assignment tests were carried out to investigate measures of gene flow. Inferences concluded that this natural heritage is not currently threatened by inbreeding or by random genetic drift. Correlation studies investigated possible effects of spatial distribution and environmental conditions on genetic structure. A climatic trend corresponding to a temperature–humidity gradient correlated significantly with the level of genetic diversity, while the edaphic variation did not.     

Population Genetic Structure of the Endangered <Emphasis Type="Italic">Brasenia schreberi</Emphasis> in South Korea Based on Nuclear Ribosomal Spacer and Chloroplast DNA Sequences

Genetic variation of nuclear ribosomal ITS (nrITS) and chloroplast DNA (cpDNA) regions was investigated in Brasenia schreberi (Cabombaceae) to assess the population structure and to infer the evolutionary relationship among 12 populations distributed in South Korea. The combined sequence of the two regions was aligned to 2,069 bp, of which 28 sites were variable. In total, 20 genotypes were identified from 240 individuals of B. schreberi. Genotype diversity (Gd) and nucleotide diversity (Pi) on Jeju Island (Gd = 0.2511, Pi = 0.00012) were higher than those of the mainland of South Korea (Gd = 0.1358, Pi = 0.00005). The relatively low level of genetic variation of the mainland populations is associated with its higher genetic differentiation (G _ST = 0.095 on mainland and 0.039 on Jeju Island) and human activities. Minimum spanning network analysis demonstrated that the investigated populations of B. schreberi were subdivided into two geographical groups: the mainland of South Korea and Jeju Island. In addition, analysis of molecular variation showed that a large proportion (73.55%) of genetic differentiation existed between the two regions. These results strongly suggest the presence of significant barriers to gene flow between regions. Thus, the management unit for B. schreberi should be carefully designed to avoid the potential risk that can results from the admixture of individuals from the mainland and Jeju Island regions.     

Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L. collections in West Africa using simple sequence repeats marker

Knowledge of genebank and on-farm genetic diversity, particularly in an introduced crop species, is crucial to the management and utilization of the genetic resources available. Microsatellite markers were used to determine genetic diversity in 574 accessions of cacao, Theobroma cacao L., representing eight groups covering parental populations in West Africa, genebank, and farmers’ populations in Nigeria. From the 12 microsatellite markers used, a total of 144 alleles were detected with a mean allelic richness of 4.39 alleles/locus. The largest genetic diversity was found in the Upper Amazon parent population (H _nb  = 0.730), followed by the 1944 Posnette’s Introduction (H _nb  = 0.704), and was lowest in the Local parent population (H _nb  = 0.471). Gene diversity was appreciably high in the farmers’ populations (H _nb  = 0.563–0.624); however, the effective number of alleles was lower than that found in the genebank’s Posnette’s population. Fixation index estimates indicated deficiency of heterozygotes in the Upper Amazon and the Local parent populations (F _is  = 0.209 and 0.160, respectively), and excess of heterozygotes in the Trinitario parent population (F _is  = −0.341). The presence of inbreeding in the Local parent populations and substructure (Wahlund effect) in the Upper Amazon were suggested for the deficiency of heterozygotes observed. Non-significant genetic differentiation observed between the genebank’s and farmers’ populations indicated significant impact of national breeding programs on varieties grown in farmers’ plantations. From this study, we showed that appreciable genetic diversity was present in on-farm and field genebank collections of cacao that can be exploited for crop improvement in West Africa. Suggestions for future conservation of on-farm genetic diversity and local landraces are further discussed.     

Genetic diversity and differentiation of <Emphasis Type="Italic">Fagus orientalis</Emphasis> Lipsky in Hyrcanian forests revealed by nuclear and chloroplast microsatellite markers

Oriental beech (Fagus orientalis Lipsky) is a widespread monoecious and wind-pollinated tree species. It is one of the major components of the Hyrcanian forests of Iran and it is of both ecological and economical importance. Twelve beech stands were surveyed at 9 chloroplast (cp) and 6 nuclear (n) polymorphic microsatellite loci (simple sequence repeats, SSR) to provide information on distribution of genetic diversity within and among populations and on gene conservation and silvicultural management of this species. High levels of genetic differentiation were detected for the chloroplast genome (F _ST = 0.80 and R _ST = 0.95), in sharp contrast to the nuclear genome (F _ST = 0.06, R _ST = 0.05). The analysis of molecular variance (AMOVA) showed that 48% of the total cpSSR variation was attributable to differences among regions and 30% to differences among populations within regions, suggesting multiple origins of beech populations in Hyrcanian forests. Nuclear SSRs confirmed the presence of significant differentiation among populations and among geographic regions, even if, as expected, this was less pronounced than that found with cpSSRs (based on AMOVA, differences among regions and among populations within regions each contribute 5% to total nSSR variance). A highly significant correlation between genetic (nSSRs) and geographic distances (R ² = 0.522) was estimated, thus showing an isolation by distance effect. The application of spatial analysis of molecular variance (SAMOVA) using both marker data allowed identification of genetically homogeneous groups of populations. Possible applications of these results for the certification of provenances and/or seed lots and for designing conservation programs are presented and discussed.     

Genetic variation and clonal structure of the rare,riparian shrub <Emphasis Type="Italic">Spiraea virginiana</Emphasis> (Rosaceae)

Genetic diversity is often considered important for species that inhabit highly disturbed environments to allow for adaptation. Many variables affect levels of genetic variation; however, the two most influential variables are population size and type of reproduction. When analyzed separately, both small population size and asexual reproduction can lead to reductions in genetic variation, although the exact nature of which can be contrasting. Genetic variables such as allelic richness, heterozygosity, inbreeding coefficient, and population differentiation have opposite predictions depending upon the trait (rarity or clonality) examined. The goal of this study was to quantify genetic variation and population differentiation in a species that resides in a highly stochastic environment and is both rare and highly clonal, Spiraea virginiana, and to determine if one trait is more influential genetically than the other. From populations sampled throughout the natural range of S. virginiana, we used microsatellite loci to estimate overall genetic variation. We also calculated clonal structure within populations, which included genotypic richness, evenness, and diversity. Gene flow was investigated by quantifying the relationship between genetic and geographic distances, and population differentiation (θ) among populations. Observed heterozygosity, genotypic richness, and inbreeding coefficients were found to be representative of high clonal reproduction (averaging 0.505, 0.1, and –0.356, respectively) and the number of alleles within populations was low (range = 2.0–3.6), being more indicative of rarity. Population differentiation (θ) among populations was high (average = 0.302) and there was no relationship between genetic and geographic distances. By examining a species that exhibits two traits that both can lead to reduced genetic variation, we may find an enhanced urgency for conservation. Accurate demographic counts of clonal species are rarely, if ever, possible and genetic exploration for every species is not feasible. Therefore, the conclusions in this study can be potentially extrapolated to other riparian, clonal shrubs that share similar biology as S. virginiana.