ALLOZYME VARIATION IN OLD WORLD RACES OF SORGHUM BICOLOR (POACEAE)

A survey of allozyme variation in cultivated races of sorghum (Sorghum bicolor) was undertaken. Eight plants each of 83 accessions representing the five primary races and five of the intermediate races of sorghum were analyzed for 15 enzyme systems encoded by 27 loci. Low levels of variation were found within accessions, which is typical of self-pollinating species. Little variation was also found among accessions. Compared with other cereals, S. bicolor is depauperate in allozyme variation. We found an average of 1.81 alleles per locus with a mean expected heterozygosity of 0.008 for the accessions and total panmictic heterozygosity of 0.093. Only 9% of the variation present was found within accessions, while 91% was among accessions. Most of the variation present is attributable to differences in geographic origin of the accessions rather than racial differences. Western and eastern Africa have the highest levels of total heterozygosity (0.108 and 0.088, respectively), while southern Africa has the lowest (0.008). Principal component analysis revealed continuous variation among races and geographic regions with the accessions failing to segregate into discrete racial or geographic clusters.     

Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers

Microsatellite markers are increasingly being used in crop plants to discriminate among genotypes and as tools in marker-assisted selection. Here we evaluated the use of microsatellite markers to quantify the genetic diversity within as well as among accessions sampled from the world germplasm collection of sorghum. Considerable variation was found at the five microsatellite loci analysed, with an average number of alleles per locus equal to 2.4 within accessions and 19.2 in the overall sample of 25 accessions. The collection of sorghum appeared highly structured genetically with about 70% of the total genetic diversity occurring among accessions. However, differentiation among morphologically defined races of sorghum, or among geographic origins, accounted for less than 15% of the total genetic diversity. Our results are in global agreement with those obtained previously with allozyme markers. We were also able to show that microsatellite data are useful in identifying individual accessions with a high relative contribution to the overall allelic diversity of the collection. Received: 10 August 1999 / Accepted: 27 August 1999     

Development of PCR-based chloroplast DNA markers that characterize domesticated cowpea (Vigna unguiculata ssp. unguiculata var. unguiculata) and highlight its crop-weed complex

In 1992, Vaillancourt and Weeden discovered a very important mutation for studying cowpea evolution and domestication. A loss of a BamHI restriction site in chloroplast DNA characterized all domesticated accessions and a few wild (Vigna unguiculata ssp. unguiculata var. spontanea) accessions. In order to screen a larger number of accessions, primers were designed to check this mutation using PCR RFLP or direct PCR methods. Using these new primers, 54 domesticated cowpea accessions and 130 accessions from the wild progenitor were screened. The absence of haplotype 0 was confirmed within domesticated accessions, including primitive landraces from cultivar-groups Biflora and Textilis, suggesting that this mutation occurred prior to domestication. However, 40 var. spontanea accessions distributed from Senegal to Tanzania and South Africa showed haplotype 1. Whereas this marker could not be used to identify a precise center of origin, it did highlight the widely distributed cowpea crop-weed complex. Its very high frequency in West Africa could be interpreted as a result of either genetic swamping of the wild/weedy gene pool by the domesticated cowpea gene pool or as the result of domestication by ethnic groups focusing primarily on cowpea as fodder.     

Allozyme variation among the spontaneous species of Sorghum section Sorghum (Poaceae)

Summary A survey of allozyme variation among the spontaneous taxa of Sorghum section Sorghum was undertaken. Eight plants each of 90 accessions representing the diploid S. bicolor (ssp. arundinaceum and drummondii) and the tetraploids S. almum and S. halepense were analyzed for 17 enzyme systems encoded by 30 loci. Low levels of variation were found within and among accessions, although there was more variation than is typical of inbreeding species. We found an average of 3.2 alleles per locus in ssp. arundinaceum, with a mean expected heterozygosity for the accessions of 0.034 and total panmictic heterozygosity of 0.154. An analysis of the apportionment of genetic variation among accessions of ssp. arundinaceum indicated that 26% of the variation occurs within accessions and 74% among accessions. Cultivated sorghum contains far less allozymic variation than ssp. arundinaceum, its presumed progenitor. This is consistent with the prediction that cultivated sorghum experienced a loss of genetic variation during domestication. For the most part, cultivated sorghum contains a subset of the allozymes found in ssp. arundinaceum. Principal component analysis revealed continuous variation among the accessions and geographic regions, with accessions failing to segregate into discrete clusters. However, accessions of race virgatum of ssp. arundinaceum occupied one end of the continuum and were, in that sense, distinguished from the other accessions. Similarly, most accessions of S. halepense and S. almum occupied the central portion of the continuum. The allozymic data presented here are consistent with the hypothesized origin of S. halepense via autopolyploidy or segmental allopolyploidy.     

CHLOROPLAST DNA POLYMORPHISM SUGGESTS NIGERIAN CENTER OF DOMESTICATION FOR THE COWPEA,VIGNA UNGUICULATA (LEGUMINOSAE)

Twenty-one independent chloroplast DNA polymorphisms were identified in Vigna unguiculata defining 19 different chloroplast DNA molecules (plastome types). Two plastome types, differing by a single character, were found among 32 accessions of cultivated cowpea (Vigna unguiculata ssp. unguiculata). Eighteen different plastome types were found among 26 accessions of wild cowpea (V. unguiculata ssp. dekindtiana). The very low level of chloroplast DNA diversity found in cultivated accessions relative to wild cowpea suggests that 1) the domesticated form was derived from a narrow selection of the wild germplasm and 2) chloroplast gene flow between wild and cultivated types has been very limited. Cladistic analysis of the cpDNA data generated a robust tree completely lacking homoplasy. Three wild accessions from Nigeria possessed a plastome type indistinguishable from one present in cultivated accessions, suggesting that Nigeria represents one center of domestication of the cowpea. The other plastome type within the cultivated germplasm was not found among wild accessions.     

Population Genetic Structuring in <Emphasis Type="Italic">Acanthopagrus butcheri</Emphasis> (Pisces: Sparidae): Does Low Gene Flow Among Estuaries Apply to Both Sexes?

Acanthopagrus butcheri completes its entire life history within estuaries and coastal lakes of southern Australia, although adults occasionally move between estuaries via the sea. Consequently, it is expected that populations of A. butcheri in different estuaries will be genetically distinct, with the magnitude of genetic divergence increasing with geographic isolation. However, previous genetic studies of A. butcheri from southeast Australia yielded conflicting results; allozyme variation exhibited minimal spatial structuring (θ = 0.012), whereas mitochondrial DNA distinguished the majority of populations analyzed (θ = 0.263) and genetic divergence was positively correlated with geographic isolation. This discrepancy could reflect high male gene flow, which impacts nuclear but not mitochondrial markers. Here we estimated allele frequencies at five nuclear microsatellite loci across 11 southeast Australian populations (595 individuals). Overall structuring of microsatellite variation was weaker (θ = 0.088) than that observed for mitochondrial DNA, but was able to distinguish a greater number of populations and was positively correlated with geographic distance. Therefore, we reject high male gene flow and invoke a stepping-stone model of infrequent gene flow among estuaries for both sexes. Likewise, management of A. butcheri within the study range should be conducted at the scale of individual or geographically proximate estuaries for both sexes. The lack of allozyme structuring in southeast Australia reflects either the large variance in structuring expected among loci under neutral conditions and the low number of allozymes surveyed or a recent colonization of estuaries such that some but not all nuclear loci have approached migration-drift equilibrium.     

Reproductive and genetic characteristics of rare,disjunct pitch pine populations at the northern limits of its range in Canada

Pitch pine, Pinus rigida Mill., is a rare species in Canada, existing as a disjunct population in the St. Lawrence River Valley in eastern Ontario and two northern outlier stands in southern Quebec along Canada's southern border with the United States. Reproductive and genetic characteristics of these small, scattered stands were investigated to develop a foundation for management and restoration in the event of range expansion northwards under anticipated climate warming. Seed yields and seed quality appear to be comparable to other eastern conifers, and to pitch pine at the center of its geographic range. For seed and seedling growth traits, most of the variation was attributable to differences among trees within stands and, to a lesser extent, among stands within a population; whereas the population effect was non-significant. For reproductive traits, such as numbers of filled and empty seeds per cone, reproductive efficiency, and inbreeding estimates, high levels of variation (ranging from 26% to 33%) were found among stands, suggesting that stand structural features, such as stand size and tree density within stands, play an important role in pollination environment and overall reproductive success. Estimates of genetic diversity at 32 allozyme gene loci indicate that these small, isolated stands have maintained relatively high levels of genetic diversity compared with populations at the center of its geographic range, and also relative to other widely dispersed eastern conifers. The relatively high levels of viable seed production and genetic diversity in native pitch pine populations indicate that native Canadian populations may be suitable seed sources for species restoration and range expansion in Canada.     

Assessment of genetic relationships between Setaria italica and its wild relative S. viridis using AFLP markers

AFLP markers were used to assess genetic diversity and patterns of geographic variation among 39 accessions of foxtail millet (Setaria italica) and 22 accessions of green foxtail millet (S. viridis), its putative wild progenitor. A high level of polymorphism was revealed. Dendrograms based on Nei and Li distances from a neighbour joining procedure were constructed using 160 polymorphic bands. Bootstrap values revealed that no specific geographic structure can be extracted from these data. The high level of diversity among Chinese accessions was consistent with the hypothesis of a centre of domestication in China. The results also showed that accessions from Eastern Europe and Africa form two distinct clusters. The narrow genetic basis of these two gene pools may be the result of local-adaptation. Received: 1 June 1999 / Accepted: 16 September 1999     

GENETIC DIVERSITY AND POPULATION STRUCTURE IN CAMELLIA JAPONICA L. (THEACEAE)

Camellia japonica is a widespread and morphologically diverse tree native to parts of Japan and adjacent islands. Starch gel electrophoresis was used to score allelic variation at 20 loci in seeds collected from 60 populations distributed throughout the species range. In comparison with other plant species, the level of genetic diversity within C. japonica populations is very high: 66.2% of loci were polymorphic on average per population, with a mean number of 2.16 alleles per locus; the mean observed and panmictic heterozygosities were 0.230 and 0.265, respectively. Genotypic proportions at most loci in most populations fit Hardy-Weinberg expectations. However, small heterozygote deficiencies were commonly observed (mean population fixation index = 0.129). It is suggested that the most likely cause of the observed deficiencies is population subdivision into genetically divergent subpopulations. The overall level of population differentiation is greater than is typically observed in out-breeders: The mean genetic distance and identity (Nei's D and I) between pairs of populations were 0.073 and 0.930, respectively, and Wright's Fst was 0.144. Differences among populations appeared to be manifested as variation in gene frequencies at many loci rather than variation in allelic composition per se. However, the patterns of variation were not random. Reciprocal clinal variation of gene frequencies was observed for allele pairs at six loci. In addition, principal components analysis revealed that populations tended to genetically cluster into four regions representing the geographic areas Kyushu, Shikoku, western Honshu, and eastern Honshu. There was a significant relationship between genetic and geographic distance (r = 0.61; P < 0.01). Analysis of variance on allozyme frequencies showed that there was approximately four times as much differentiation among populations within regions, as among regions. It is likely that the observed patterns of population relationships result from the balance between genetic drift in small subpopulations and gene flow between them.     

Regional structuring of genetic variation in short-lived rock pool populations of Branchipodopsis wolfi (Crustacea: Anostraca)

The genetic structure of three metapopulations of the southern African anostracan Branchipodopsis wolfi was compared by analysing allozyme variation at four loci (PGM, GPI, APK, AAT). In total, 17 local populations from three sites (metapopulations) were analysed from rock pools in south-eastern Botswana ranging from 0.2 to 21 m² in surface area. In three populations we found significant deviations from Hardy-Weinberg (H-W) equilibrium at one or more loci due to heterozygote deficiencies. Genetic variability at one site was significantly lower than at the other sites, which may be linked to a greater incidence of extinction and recolonisation, as the basins at this site are shallower and have shorter hydrocycles. Across all local populations, a significant level of population differentiation was revealed. More than 90% of this variation was explained by differentiation among sites (metapopulations), although this differentiation did not correlate with geographic distance, or with environmental variables. Genetic differentiation among populations within metapopulations was low, but significant at all sites. At only one of the sites was a significantly positive association measured between genetic and geographic distance among local populations. Our data suggest that persistent stochastic events and limited effective long-range dispersal appear to dominate genetic differentiation among populations of B. wolfi inhabiting desert rock pools. The lack of association between geographic distance and genetic or ecological differences between rock pool sites is indicative of historical stochastic events. Low heterozygosity, the significant deviations from H-W equilibrium, and the large inter- but low intra-site differentiation are suggestive of the importance of short-range dispersal. Gene flow between metapopulations of B. wolfi appears to be seriously constrained by distances of 2 km or even less. Received: 28 June 1999 / Accepted: 10 January 2000     

Genetic relationships among subspecies of Vigna unguiculata (L.) Walp. based on allozyme variation

 The cowpea [Vigna unguiculata (L.) Walp.] is a morphologically and genetically variable species composed of wild perennial, wild annual, and cultivated forms that are mainly used for edible seeds and pods. In this study, genetic variation in 199 germplasm accessions of wild and cultivated cowpea was evaluated using an allozyme analysis. The results from this survey showed that wild cowpea exhibits genetic variation perfectly fitted with the existing morphological classification. The cowpea gene-pool is characterized by its unusually large size. It encompasses taxa (ranked as subspecies) that could be considered as different species considering the high genetic distances observed between accessions belonging to different taxa. These subspecies can be classified into three groups characterized by their breeding systems: perennial outcrossers, perennial out-inbreds, and inbred annuals. Allozyme data confirm this grouping. Perennial outcrossers look primitive and are more remote from each other and from perennial out-inbreds. Within this large gene-pool, mainly made of perennial taxa, cultivated cowpeas (ssp. unguiculata var. unguiculata) form a genetically coherent group and are closely related to annual cowpeas (ssp. unguiculata var. spontanea) which may include the most likely progenitor of cultivated cowpeas. Received: 15 June 1998 / Accepted: 29 September 1998     

Genetic structure of Glycine canescens,a perennial relative of soybean

Summary Allozyme variation as detected by starch gel electrophoresis was used to assess the extent and spatial organization of genetic variation across the entire range of Glycine canescens sensu lato. Eleven enzyme systems were assayed in 116 accessions of this taxon and 102 alleles were detected at a total of 31 loci. Eighty-one percent of loci were polymorphic. Most of this variation occurred between and very little within accessions. Three major groupings were detected. These groupings (groups 1, 2, and 3) also differed with respect to mean seed size and their geographic distribution. A further ten accessions stood out from these distinct groups. These accessions were most closely related to group 3 but were variable among themselves. In general, they were collected from highly dissected terrain, often in the remote interior of the continent. A final group of 18 problematic accessions (group X), originally tentatively identified as G. canescens on morphological grounds, was shown to be isozymically distinct from this species and was reclassified as one form of the polytypic species G. clandestina.     

Allozyme differentiation of populations of the dogwhelk Nucella lapillus, (L.): the relative effects of geographic distance and variation in chromosome number

Geographic patterns of genie differentiation were compared with differentiation between karyotypes in the intertidal snail Nucella lapillus. Samples from 24 sites covering the species range in Europe and North America were analysed for allozyme variation at 16 soluble enzyme loci. Two homokaryotypes have been identified with diploid numbers 2n = 26 and 2n= 36 (variation is Robertsonian and hybrids have intermediate chromosome numbers) and samples were classified (on the basis of published data) according to karyotype. Group 1 consisted of samples from three English Channel populations of higher chromosome number (on average 2n > 32) and Group 2 consisted of the remaining 21 samples (presumed to be 2n= 26). Karyotype variation accounts for roughly the same amount of the absolute allozyme variance as geographic variation (46.3 °, and 53.7°, respectively). Yet the patterns of differentiation seen between karyotypes and with geographic separation are very different. In samples classified as 2n= 26 (Group 2), while there is a significant amount of heterogeneity (F_ST per locus averaged 0.128 for 10 polymorphic loci), allozyme variation occurs independently at different loci so mean genetic identity (Nei) is high: 0.972. There is only a slight decline in genetic identity with distance (genetic identity averaged 0.965 for amphi-atlantic comparisons) indicating that passive transport of juveniles or adults may contribute significantly to gene flow. Conversely, allozyme variation between karyotypes was concordant. High chromosome number populations possessed a suite of alleles at four allozyme loci (Esl-3, Lap-2, Mdh-1 and Pep-2) which were absent or rare in Group 2 samples resulting in high F_ST values for these loci (from 0.294 to 0.472) when karyotypic classes were combined. Consequently the mean genetic identity between these Robertsonian races is low, 0.856, and falls within the range more usually associated with congeneric comparisons than with con-specific comparisons. The mechanisms maintaining this genie difference are unclear. However the distribution of the karyotypes and physiological and morphological differences (in shell shape) between them strongly suggest that karyotypic variation in Nucella is adaptive.     

GEOGRAPHICAL PATTERNS AND POPULATION STRUCTURE IN PERIODICAL CICADAS BASED ON SPATIAL ANALYSIS OF ALLOZYME FREQUENCIES

There are twelve major broods, or year classes, of 17-year periodical cicadas and three major broods of 13-year cicadas. Previous allozyme studies of three 13-year broods and two 17-year broods suggested that broods are distinct evolutionary units, exhibiting homogeneity within broods and heterogeneity among broods. Results from numerical phylogenetic analysis of allozyme data from these broods supported Lloyd and Dybas's (1966a, 1966b) evolutionary hypothesis and were consistent with biogeographical patterns. In the present paper, we use spatial statistics to extend the analysis of biogeographical patterns for periodical cicadas by examining geographic variation in allozyme frequencies within and among ten broods for the three most variable loci. The results from our analysis show that each gene frequency surface exhibits marked spatial autocorrelation. Three major geographic areas of similarity are indicated by the data: the eastern seaboard, the Mississippi Valley, and the eastern edge of the Great Plains. When localities are adjusted for regional membership, the autocorrelation disappears. In biological terms, broods are homogeneous breeding units. Geographically distinct localities within the same brood show little differentiation. Differentiation among populations within broods and among broods within regions exists but is less pronounced than the differentiation among geographic regions. For the particular enzymes examined, allozyme frequency differences appear to reflect the phylogenetic history of the broods rather than their environmental surroundings.     

Geographic and altitudinal allozyme variation in sorghum (Sorghum bicolor (L.) Moench) landraces from Ethiopia and Eritrea

The amount and distribution of genetic variation was investigated in 48 sorghum landrace accessions, representing 13 regions of origin and three adaptation zones (lowland, intermediate and highland elevation) in Ethiopia and Eritrea. Assaying 11 enzymes systems, 23 putative loci were scored for a total of 27 alleles. Nineteen loci were monomorphic and fixed for the same allele, while the remaining 4 loci, each with 2 alleles, were polymorphic across the 48 accessions. The results show significant differences in allele frequencies among the accessions, regions of origin and the adaptation zones. However, all measures of genetic variation used show that the accessions maintained much lower levels of variation than the corresponding mean values for self-pollinating crop plants, confirming previous conclusions that sorghum is depauperated in allozymic variation. The total gene diversity was 0.25, which partitioned 59% within and 41% among accessions. The latter was largely due to variation among accessions within the adaptation zones (38%), while only 3% was due to variation among accessions between the adaptation zones. Similarly, most of the total gene diversity was found within the regions of origin (80%) and within the adaptation zones (97%). Both the dendrogram constructed from NEI's unbiased genetic distance and the plot of the first two principal components distinguished three groups of regions. The level of gene flow was low among accessions, regions of origin and among accessions within adaptation zones, but high among adaptation zones. The results are discussed with emphasis on genetic resources conservation and utilization.     

DIFFERENTIATION AMONG NINE POPULATIONS OF PHLOX. I. ELECTROPHORETIC AND QUANTITATIVE VARIATION

The organization of genetic variation in Phlox drummondii was investigated using both allozyme electrophoresis and quantitative genetics. Variation at five polymorphic enzyme loci was characterized in nine populations, and variation in 16 morphological and life-history characters was examined using an analysis of full- and half-sibs in seven populations. Significant levels of genetic variation were found at enzyme loci and for metric characters. Significant heritabilities were observed for 15 of the 16 characters examined. Genetic differences among populations were revealed both by Nei's genetic distance and by phenotypic differences, summarized by discriminant analysis. Partitioning variance in allozyme frequencies among hierarchical levels of genetic organization indicated that 94% of this variance lay within populations, 4% between populations within varieties, and 2% between varieties. Partitioning phenotypic variance for metric characters indicated that 73% lay within populations, 24% lay between populations within varieties, and 3% lay between varieties. Thus, both electrophoretic and metric characters indicated that despite extensive genetic differentiation among populations, most of the evolutionary potential of the species lies within populations.     

Patterns of morphometric and allozyme variation in Aedes albopictus

A survey of microgeographic variation using morphometric and allozyme analyses was conducted on 19 US populations of Aedes albopictus (Skuse) (Diptera: Culicidae), a mosquito that was recently introduced into the US. There was considerable variation within and among populations both in morphometric traits and allele frequencies. A multivariate discriminant analysis enabled the separation of populations into distinct groups; separation among the populations in the morphometric analysis was incomplete with an average of 70% of the individuals being correctly classified. In the allozyme analysis, the discrimination was complete. The populations from Texas were placed close together in the morphometric analysis, whereas in the allozyme analysis a geographic clustering of populations could not be detected. A test of association between the distance matrices derived from the morphometric and allozyme analyses was statistically nonsignificant. The results are discussed in the context of the colonization of the US by A. albopictus. The possible factors underlying the differences in the patterns of variation derived from morphometric and allozyme analyses are also discussed.     

Allozyme evidence for the origin and diversification of Gossypium barbadense L.

Summary Gossypium barbadense L. is a commercially important cotton species of tropical South American origin presently grownin many regions of the world. The species is morphologically diverse, consisting of a wide range of wild (or feral), commensal, landrace, and highly improvedcommercial forms. We performed allozyme analysis on 153 accessions representing the spectrum of G. barbadense diversityto ascertain the geographic origin of the species, its patterns of diffusion subsequent to domestication, and to reveal infraspecific relationships. Levels ofgenetic variation in G. barbadense are moderate. Of 59 loci scored, 24 were polymorphic, with a mean number of alleles perlocus of 1.69 and an average panmictic heterozygosity of 0.062. Principal component analysis revealed geographic clustering of accessions into six relativelydiscrete regions. Gene frequencies at many loci are significantly heterogeneous among these regions, with an average G _STof 0.272. Northwestern South America contains the greatest genetic variability; we suggest that this region is the ancestral home of the species. The data indicate separate diffusion pathways from this region into Argentina-Paraguay and into eastern and northern South America east of the Andes. Caribbean Island and Central American forms appear to be derived from the latter. These diffusion pathways are in accordance with morphological evidence and historical record. In contrast to expectations based on geographic proximity, Pacific Island forms have their closest affinity to accessions from eastern South America. Advanced cultivated stocks seem largely derived from western Andean material, but also contain introgressed G. hirsutum germ plasm. Introgression was relatively high (22%–50% of accessions) in commercial stocks and in forms from Argentina-Paraguay and various Pacific Islands, but was conspicuously low or absent in material from Central America and the Caribbean, where commensal and commercial forms of both species are sympatric.     

Analysis of F ST outliers at allozyme loci in Pacific salmon: implications for natural selection

Natural selection has been invoked to explain the observed geographic distribution of allozyme allele frequencies for a number of teleost species. The effects of selection on allozyme loci in three species of Pacific salmon were tested. A simulation-based approach to estimate the null distribution of population differentiation (F _ST) and test for F _ST outliers was used. This approach showed that a majority of allozyme loci conform to neutral expectations predicted by the simulation model, with relatively few F _ST outliers found. No consistent F _ST outlier loci were found across species. Analysis of population sub-groups based on geography and genetic identity reduced the number of outlier loci for some species, indicating that large geographic groups may include genetically divergent populations and/or that there is geographic heterogeneity in selection pressure upon allozyme loci. Two outlier allozyme loci found in this analysis, lactate dehydrogenase-B and malic enzyme, have been shown to be influenced by selection in other teleost species. This approach is also useful in identifying allozyme loci (or other genetic markers) that meet assumptions for population genetic study.