Genetic diversity and multilocus associations in Cunninghamia lanceolata (Lamb.) Hook from The People's Republic of China

Open-pollinated seeds were assayed for allozyme polymorphisms at 24 loci to assess genetic diversity and multilocous associations in 16 populations of Cunninghamia lanceolata (Lamb.) Hook in the People's Republic of China. On average, the percentage of polymorphic loci was 88.0, the number of alleles per locus was 3.0, and the expected heterozygosity was 0.394. The distribution of genetic diversity was not correlated with the geographic and climatic variables of the populations. However, allele frequencies correlated linearly with the mean annual temperature of the populations at Mdh-1, Mdh-2, Mnr-2, Pgi-1, and Skdh-1 and with the altitude of the populations at Aph-4 and 6Pg-2. Of the total gene diversity 6% was attributed to among-population differentiation; 94% resided within populations. Two-locus gametic disequilibria were found in 15 of the 16 populations, and higher-order gametic disquilibria were significant in most populations. The gametic disequilibria did not correlate with geographic and climatic variables. The results suggest that population subdivision, founder effect, occurrence across diverse environments, a mating system dominated by inbreeding, and historical events from 2000 years of cultivation are contributing factors in the generation and maintenance of the multilocus genetic structure in this conifer.     

Variation on reaction norm in lodgepole pine natural populations

Variations on the norm of reaction among ten natural lodgepole pine populations sampled from three lodgepole pine subspecies (Pinus contorta ssp. contorta, ssp. latifolia and ssp. murrayana) were studied by using 20 year heights measured in 57 provenance test sites across interior British Columbia (B.C.). There were significant population by site interactions. Concurrent joint regression and the AMMI model were used to dissect these population by environmental interactions. Joint regression analysis indicated that three populations (from the northwest) had a negative linear regression coefficient with environmental deviation, three (from central and southeast sites) had a positive regression coefficient and four (from the southwest) had a zero regression coefficient. The AMMI model revealed a similar pattern of reaction norm among the ten populations. But the three significant IPCA axes, which captured twice as much of the G × E sum of squares than joint regression, were more effective in separating the ten populations and associating their performance with the climate of test sites and their origin. The variation patterns of reaction norm in lodgepole pine populations demonstrated that adaptation of lodgepole pine natural populations to the various physical environments, at sub-species as well as at population level, was due largely to a balance between selection for high growth potential in less severe environments and selection for high cold hardiness in severe environments. Received: 4 May 2000 / Accepted: 10 November 2000     

The Genetical Response to Natural Selection by Varied Environments. IV. Gametic Disequilibrium in Spatially Varied Environments

Gametic disequilibria between allozyme loci were related to spatial variation of the environment in caged populations of Drosophila melanogaster . Two experiments, one with flies collected at "Chateau Tahbilk," South Australia, and the other with flies from "Groningen," The Netherlands, were sampled at generations 16 and 32. Spatial variation of the environment was stimulated using three food media. Eight polymorphic allozyme loci were used to estimate gametic disequilibria from digenic combinations of allotypes. All populations were duplicated within an environment and maintained at about 2500 adults. Standardized gametic disequilibria were compared by a weighted least squares analysis of the z-transformed statistical correlation of allele frequencies. Gametic disequilibria were strongly dependent upon food niche and food-niche interactions. The effects also varied with sampling time and were similar in duplicate populations. Gametic disequilibria were most often detected in the "Groningen"-derived populations and their strength was not strongly associated with recombination fraction. Many of the disequilibria concerned unlinked loci. The strength of selection was probably considerable and populations were evolving genetic architectures which reflected niche selection by the different foods without marked genetic isolation between foods; gene frequencies did not vary between niches within a population cage.     

EVOLUTION OF THE PYGMY-FOREST EDAPHIC SUBSPECIES OF PINUS CONTORT A ACROSS AN ECOLOGICAL STAIRCASE

Patterns of allozyme variation within and between two of the subspecies of Pinus contorta were examined for the evolutionary relationship between them. In coastal northern California, these subspecies are parapatric. Pinus contorta ssp. contorta occurs on grassy coastal bluffs on the lowest and youngest of a sequence of five marine terraces; P. contorta ssp. bolanderi is endemic to a pygmy forest ecosystem that occurs on the increasingly older and harsher soils of the third, fourth, and fifth terraces. The soils of the upper three terraces are characterized by extreme podzolization, low pH, low nutrient availability, summer drought (with periodic fires), and winter surface flooding above the hardpan. Dune and cliff soils support a tall redwood and Douglas-fir forest between the terraces. Analyses of seeds collected from 11 pygmy-forest and 6 coastal populations showed ssp. bolanderi to have significantly less allozyme variation than spp. contorta. The two subspecies did not show the phylogenetic dichotomy in allozyme allelic constitutions expected for subspecific classification. Within ssp. bolanderi, the pattern of genetic distances correlated better with edaphic differences among sites than with geographic distance. It appears that ssp. bolanderi is a recently evolved derivative of ssp. contorta, and that the low degree of allozyme differentiation among the bolanderi populations may be due to colonization of the sites by small numbers of individuals, or to hitchhiking of allozyme loci linked to loci undergoing strong selection imposed by the severe edaphic conditions typical of bolanderi sites.     

Genetic and clonal diversity in Korean populations ofVitex rotundifolia (Verbenaceae)

Vitex rotundifolia L.f. is a woody perennial and has sexual and asexual modes of reproduction. Allozyme study was conducted on 550 plants in 13 Korean populations. The levels of genetic variability and divergence within and among populations, respectively, are considerably lower and higher than the mean values for woody plants with similar life history tralts. Mean percentage of polymorphic loci (P _P), mean number of alleles per locus (A _P), and mean genetic diversity (He _P) within populations ofV. rotundifolia were: 16.7%, 1.21, and 0.047. On average, about 79% of the total variation inV. rotundifolia was common to all populations (meanG _ST=0.208). In addition, significant differences in allele frequencies among populations were found in all polymorphic loci examined (P<0.001). On the other hand, levels of genotypic diversity within and among populations were moderate. About 44% (18/41) of multilocus genotypes were “local genotypes” (genotypes occurring in only one population), whereas only one “widespread genotype” (genotypes occurring in more than 75% of the populations) were detected. The mean number of multilocus genotypes per population (G) and mean genotypic diversity index (D _G) were 8.4 and 0.74, respectively. Most common multilocus genotypes found in populations were homozygous for five polymorphic loci. The abundance of ramets of these genets is responsible for the low levels of expected heterozygosity within populations. The results indicate that clonal reproduction may act as an enhancer of genetic drift by reducing effective size of local populations ofV. rotundifolia.     

Taxonomic and population differentiation of mitochondrial diversity inPinus banksiana andPinus conforta

We have studied two mitochondrial DNA polymorphisms in 741 individuals from 16 allopatric populations ofPinus banksiana Lamb. andPinus contorta Dougl. Restriction fragments of both polymorphisms distinguished the two species qualitatively, except in aP. Banksiana population whose ancestors were involved in hybridization withP. contorta.COXI-associated restriction fragments were monomorphic within species, whileCOXII-associated restriction fragments were highly variable inP. contorta (H_es=0.68). Population differentiation was substantial inP. contorta (F_st=0.31 among subspecies; mean F_st=0.66 within subspecies) and consistent with predictions for maternally inherited markers. Plant mitochondrial markers appear to be useful for the investigation of seed migration routes, hybridization and introgression, breeding zone designation, and the development of germ plasm conservation sampling strategies.     

Genetic variation and population structure of endemic yellow catfish, <Emphasis Type="Italic">Horabagrus</Emphasis><Emphasis Type="Italic">brachysoma</Emphasis> (Bagridae) among three populations of Western Ghat region using RAPD and microsatellite markers

Random amplified polymorphic DNA (RAPD) and microsatellite markers were applied to evaluate the genetic variation in endemic and endangered yellow catfish, Horabagrus brachysoma sampled from three geographic locations of Western Ghat, South India river systems. In RAPD, of 32 10-mer RAPD primers screened initially, 10 were chosen and used in a comparative analysis of H. brachysoma collected from Meenachil, Chalakkudy and Nethravathi River systems. Of the 124 total RAPD fragments amplified, 49 (39.51%) were found to be shared by individuals of all 3 populations. The remaining 75 fragments were found to be polymorphic (60.48%). In microsatellites, six polymorphic microsatellite loci were identified by using primers developed for Pangasius hypophthalmus, Clarias macrocephalus and Clarias gariepinus. The identified loci were confirmed as microsatellite by sequencing after making a clone. The nucleotide sequences of 6 loci were published in NCBI genbank. The number of alleles across the six loci ranged from 4 to 7 and heterozygosities ranged from 0.07 to 0.93. The mean number of alleles and effective number of alleles per locus were 5.00 and 3.314, respectively. The average heterozygosity across all investigated samples was 0.72, indicating a significant deficiency of heterozygotes in this species. RAPD and microsatellite methods reported a high degree of gene diversity and genetic distances depicted by UPGMA dendrograms among the populations of H. brachysoma.     

Genetic variability in Plantago species in relation to their ecology

Summary A survey of enzyme variability in several populations of Plantago major in the Netherlands has been made. Nine of 36 loci were found to be polymorphic. The most extensively studies population showed 7 polymorphic loci (19%). The average heterozygosity was 0.005, a low value since P. major is predominantly inbreeding; a first estimate of the outcrossing rate is only 10%. All nine variable loci show simple Mendelian inheritance, seven of them could be placed into four different linkage groups. Marked differences in allele frequencies were found between two subspecies: ssp. major and ssp. pleiosperma. Two enzyme loci possess subspecies-specific alleles, Pgm-1 and Got-1. The most likely explanation of this phenomenon is the existence of fitness differences, caused either by the enzyme loci themselves or by linked loci.Grassland Species Research Group Publication no. 14     

Isolation and characterization of polymorphic microsatellite markers for the endangered tree <Emphasis Type="Italic">Handeliodendron bodinieri</Emphasis> (Sapindaceae)

Nine polymorphic microsatellite loci were developed and characterized for Handeliodendron bodinieri, an endangered tree endemic to karst forest in southwest China. Each locus displayed between 4 and 11 alleles. The observed heterozygosity ranged from 0.345 to 0.931 and expected heterozygosity varied from 0.414 to 0.824. The combined probabilities of paternity exclusion over all loci were 0.931 for P _r(Ex₁) and 0.993 for P _r(Ex₂), respectively. These loci represent a powerful tool in investigating gene flow and population structure in natural populations of H. bodinieri.     

Allozyme Variation and Phylogenetic Relationships in Picea jezoensis (Pinaceae) Populations of the Russian Far East

Genetic variation and differentiation of 12 populations of Picea jezoensis from the Russian Far East were studied using 20 allozyme loci. The mean number of alleles per locus was 2.63, the percent of polymorphic loci was 88.1%, the observed heterozygosity was 0.181, and the mean value of expected heterozygosity amounted to 0.189. The values of expected heterozygosity of the northern and central mainland populations were higher than in the southern part of the natural range. A significant bias of Hardy–Weinberg heterozygosity to equilibrium heterozygosity (H_eq) suggests that most of the mainland populations have recently experienced a severe expansion in population size while populations from Kamchatka Peninsula have undergone a reduction in population size. Unbiased Nei’s genetic distance values were low within and between the mainland and Sakhalin Island populations (D_N=0.008). The largest values (D_N=0.063) were found between the mainland/Sakhalin and Kamchatka Peninsula populations. Based on genetic distance, P. jezoensis and P. kamtschatkensis could be considered as distinct taxa, but P. ajanensis, P. microsperma, and P. komarovii do not warrant taxonomic recognition.     

Genetic variation within and between populations of hermaphroditic <Emphasis Type="Italic">Bulinus truncatus</Emphasis> tetraploid freshwater snails of the Albertine Rift,East Africa

Genetic variability within and among Bulinus truncatus of the Albertine Rift freshwater bodies were assessed to investigate the degree of inbreeding and gene flow in the snail populations. The effect of ploidy on the genetic structuring of B. truncatus is also described. We characterized the genetic structure of seven B. truncatus populations from Lake Albert, Lake Kivu, and Katosho swamp in Tanzania using five polymorphic microsatellite loci. Genetic differentiation was quantified using pairwise FST values and Nei’s standard genetic distances. Different alleles were observed across all loci and genetic diversity was low although it varied greatly across populations; observed heterozygosity was, however, higher than the expected heterozygosity in three of the populations studied. Significant heterozygote deficiencies were observed coupled with significant linkage disequilibria in five populations for all the five loci examined in this study. We found significant genetic differentiation among the seven freshwater bodies; private alleles were observed across all loci indicating restricted or absence of gene flow between populations. Limited snail dispersal and the reproductive biology of B. truncatus are the major forces shaping the genetic variation observed. Low genetic variation within B. truncatus populations exposes them to a high parasite infection risk as predicted in the Red Queen hypothesis.     

Multilocus Structure of Natural Populations of HORDEUM SPONTANEUM

The association of alleles among different loci was studied in natural populations of Hordeum spontaneum, the evolutionary progenitor of cultivated barley. The variance of the number of heterozygous loci in two randomly chosen gametes affords a useful measure of such association. The behavior of this statistic in several particular models is described. Generally, linkage (gametic phase) disequilibrium tends to increase the variance above the value expected under complete independence. This increase is greatest when disequilibria are such as to maximize the sum of squares of the two-locus gametic frequencies.—When data on several loci per individual are available, the observed variance may be tested for its agreement with that expected under the hypothesis of complete interlocus independence, using the sampling theory of this model. When applied to allozyme data from 26 polymorphic populations of wild barley, this test demonstrated the presence of geographically widespread multilocus organization. On average, the variance was 80% higher than expected under random association. Gametic frequencies for four esterase loci in both of these populations of wild barley and two composite crosses of cultivated barley were analyzed. Most generations of the composites showed less multilocus structure, as measured by the indices of association, than the wild populations.     

Genetic diversity and climatic determinants of tree frogs in Israel

Summary Allozymic variation in proteins encoded by 27 loci was analyzed electrophoretically in 218 adult specimens, mostly males, representing 8 populations, 5 central and 3 marginal, of lemon yellow treefrogs, Hyla arborea savignyi, in Israel along two transects of increasing aridity: (a) north to south and (b) west to east. The results indicate that (a) Of the 27 loci examined, 5 are monomorphic in all 8 populations; 9 are locally and weakly polymorphic; 6 are regionally and weakly polymorphic; and 7 are regionally and strongly polymorphic; (b) In the populations studied, no alternative fixations were found in any of the 27 loci, except in the Wasit population. The commonest allele predominates across all populations, except Wasit, central as well as marginal; (c) Clinal patterns associated with increasing aridity southwards and eastwards occur in polymorphism, P, heterozygosity, H, and in allele frequencies of Ldh-1, Fum, Got-1, and Sdh; (d) For habitat generalists, treefrogs have above average number of alleles per locus, A, and polymorphism, P, while the heterozygosity, H, is average. All three estimates A, P, and H exhibit wide geographic variation decreasing progressively southwards and eastwards; (e) Central populations harbor more genic variation then marginal populations; (f) Genic similarity between populations is high; (g) Significant gametic phase disequilibria were found in several tests in 2 populations; (h) P, H, and allozymic variation in several gene loci are significantly correlated and predictable by environmental variables, primarily those related to water; (i) Morphological and allozymic variations are uncorrelated.The spatial patterns and environmental correlates and predictors of genic variation in Hyla arborea savignyi in Israel suggest that (i) protein polymorphisms are largely adaptive and are molded primarily by climatic selection rather than by stochastic processes or neutrality, and (ii) the environmental variation model seems to be the best predictor of genic variation in treefrogs.     

Characterization of microsatellite loci developed for <Emphasis Type="Italic">Amaranthus hypochondriacus</Emphasis> and their cross-amplifications in wild species

The present study reports isolation and characterization of 12 polymorphic microsatellite markers for Amaranthus hypochondriacus. A total of 92 alleles were detected across the 20 accessions, with an average of 7.7 alleles per locus. The observed (H _O ) and expected (H _E ) heterozygosity values ranged from 0 to 0.95 and from 0.49 to 0.92, respectively. At significance threshold (P < 0.05), nine loci deviated from Hardy-Weinberg equilibrium (HWE), whereas significant linkage disequilibria (LD) were observed between five pairs of loci. The 12 loci were successfully amplified in 18 other amaranth species representing cultivated grain and vegetable species, their putative progenitors and wild species. These results demonstrate wide potential applicability of these markers for the study of intra- and inter-specific genetic diversity as well as evolutionary relationships among cultivated and wild amaranths.     

Conservation of genetic diversity in British populations of the diploid endemic Coincya monensis ssp monensis (Isle of Man Cabbage): the risk of hybridisation with the tetraploid alien, Coincya monensis ssp cheiranthos

Coincya monensis is represented in the British flora by two, cytologically distinct subspecies. Coincya monensis ssp monensis is an endemic diploid with a coastal sand dune distribution that includes a number of isolated populations. Coincya monensis ssp cheiranthos is a tetraploid alien, well established in South Wales in early successional habitats. Both subspecies share similar life form traits, flowering times and pollinators. Cluster analysis and phylogenetic reconstruction based on sequences of the mitochondrial nad4 gene confirmed the distinction between alien and endemic taxa. Tetraploid populations carry more polymorphic RAPDs loci and their genetic diversity is partitioned more within than among populations. In contrast, C. monensis ssp monensis has a distinct population genetic structure. Analysis of the multilocus genetic data confirmed a structure of genetically isolated, endemic population clusters in Scotland, Arran, the Isle of Man and South Wales. Experimental hybridisation showed the two subspecies are interfertile. Multivariate analysis of RAPDs data resolved hybrids between alien and endemic clusters and hybrids contained a proportion of alien-specific polymorphic loci. Hybrids of alien maternal parentage contained the mitochondrial nad4 sequence characteristic of the alien subspecies. Since the alien subspecies can invade mobile sand dune communities from urban sites and compete for pollinators, there is a risk that alien and endemic populations will mix and introgress. Conservation of endemic genetic diversity in Britain will require protection for all C. monensis ssp monensis populations. Currently, the most disjunct endemic population in South Wales is most at risk from introgression.     

Isolation and characterization of highly polymorphic microsatellite loci in Schreibers’ long‐fingered bat,Miniopterus schreibersii (Chiroptera: Vespertilionidae)

Five polymorphic, dinucleotide microsatellite loci have been identified and characterized in Schreibers’ long‐fingered bat, Miniopterus schreibersii (Chiroptera: Vespertilionidae). These include three uninterrupted (CA)_n repeats, ranging in length from (CA)₁₇ to (CA)₁₉, one interrupted repeat (CA)₄(CG)₂(CA)₁₃, and one uninterrupted (GA)₂₇ repeat. All loci were highly polymorphic, with 17–20 alleles identified per locus. Observed heterozygosity levels (0.66–0.82) are lower than expected due to homozygote excess, probably caused by pooling of populations, resulting in population substructuring. All five polymorphic loci were also successfully amplified in the closely related M. fraterculus. Two pairs of primers additionally amplified polymorphic microsatellites in Chaerophon sp.     

Analysis of genetic diversity in Glyptosternum maculatum (Sisoridae, Siluriformes) populations with AFLP markers

We determined the genetic diversity of geographic populations from three spawning grounds (Nyang River, Lhasa River, Shetongmon Reach of Yarlung Zangbo River) of Glyptosternum maculatum with amplified fragment length polymorphism (AFLP) markers. Five primer combinations detected 332 products, 51 of them (15.4%) were polymorphic in at least one population. The Shetongmon population was found to be the richest in genetic diversity as was indicated by the percentage of polymorphic loci and heterozygosity, followed by the Nyang population and the Lhasa population. The pair-wise genetic distance between populations were all very close, ranging from 0.0015 to 0.0042 with an average of 0.0024. The genetic distance was not proportional to the geographic distance. The analysis of molecular variance demonstrated that all variation occurred within populations. The average estimated fixation index (F _st) of three populations across all polymorphic loci was −0.0184, indicating the absence of genetic differences among the three sampled populations. The differentiation among populations was not significant, and population structure was weak. Our observations will help identify the genetic relationship among populations as the first approach to understand the genetic diversity of Glyptosternum maculatum.     

Isolation and characterization of microsatellite loci from three cryptic species of Ceratosolen emarginatus

From an enriched (AG)_n/(AC)_n library, we developed nine polymorphic microsatellite loci for three cryptic species of the fig‐pollinating wasp Ceratosolen emarginatus. We genotyped one population for each of the three cryptic species across all the nine loci. In total, 204 alleles were detected from the three cryptic species of C. emarginatus. The observed heterozygosity was 0.755 ± 0.034, 0.653 ± 0.030 and 0.603 ± 0.073 in C. emarginatus populations A, B and C, respectively; the expected heterozygosity was 0.850 ± 0.031, 0.724 ± 0.035 and 0.702 ± 0.104, respectively. No linkage disequilibrium was found between any two loci of all three cryptic species. The newly isolated microsatellite markers will be very useful for estimating the genetic variation within and among the cryptic species and for revealing the mechanisms of speciation and inbreeding coexistence hypothesis of the cryptic species.     

Genetic divergence between Melipona quadrifasciata Lepeletier (Hymenoptera,Apidae) populations

Melipona quadrifasciata is a stingless bee widely found throughout the Brazilian territory, with two recognized subspecies, M. quadrifasciata anthidioides, that exhibits interrupted metasomal stripes, and M. quadrifasciata quadrifasciata, with continuous metasomal stripes. This study aimed to estimate the genetic variability of these subspecies. For this purpose, 127 colonies from 15 Brazilian localities were analyzed, using nine species-specific microsatellite primers. At these loci, the number of alleles ranged from three to 15 (mean: 7.2), and the observed heterozygosity (H_o) ranged from 0.03–0.21, while the expected heterozygosity (H_e) ranged from 0.23–0.47. The genetic distances among populations ranged from 0.03–0.45. The F_ST multilocus value (0.23) indicated that the populations sampled were structured, and the clustering analysis showed the formation of two subgroups and two more distant populations. The first group contained the subspecies M. quadrifasciata quadrifasciata, and the other, the subspecies M. quadrifasciata anthidioides and the two M. quadrifasciata populations with continuous metasomal stripes from northern Minas Gerais. These results confirmed that the yellow metasomal stripes alone are not a good means for correctly identifying the different subspecies of M. quadrifasciata.     

Population genetic analysis of Elliottiaracemosa (Ericaceae), a rare Georgia shrub

Genetic and genotypic diversity found within populations of threatened plant species can have important implications for their conservation and management. In this study we describe genetic and genotypic diversity found within 10 populations of the endemic shrub Elliottiaracemosa (Ericaceae), the Georgia plume. E. racemosa is a threatened species known from fewer than 50 locations, all within the state of Georgia, USA. Seedset is limited to nonexistent in some E. racemosa populations and sexual recruitment has not been documented. However, the species is known to spread vegetatively via root-sprouts. Twenty-one allozyme loci were resolved for E. racemosa, nine of which were polymorphic. Compared with other woody taxa, E. racemosa has low genetic (i.e. allelic) diversity within populations (H_ep = 0.063) and at the species level (H_es = 0.091). Most of the genetic variation (82%) was found within populations, and genetic identities between populations were high (mean I = 0.96). However, genotypic diversity (i.e. the number of multilocus genotypes) differed markedly among populations. Two of the 10 populations consisted almost entirely of single multilocus genotypes, whereas more than 20 multilocus genotypes (in samples of 48 stems) were detected at three sites. Sites in which few multilocus genotypes were detected have low seedset, suggesting that the lack of clonal diversity limits reproduction in some populations of this reportedly self-incompatible species.