The patterns of genetic diversity in Carpentaria acuminata (Arecaceae), and rainforest history in northern Australia

Carpentaria acuminata occurs in monsoon rainforest and is endemic to the Northern Territory, Australia. The genetic diversity of C. acuminata populations was surveyed across the geographical range of the species using isozyme analysis. Genetic diversity within C. acuminata populations ( H _E = 0.143) was typical of rainforest species and woody angiosperms generally. Genetic diversity was not correlated with rainforest patch size. However, there was significant heterogeneity among populations ( F _ST = 0.379), with infrequent effective gene flow among populations ( Nm = 0.39). Genetic diversity was negatively correlated with increasing distance between neighbouring C. acuminata populations, but geographical distance was not a good predictor of genetic similarity. C. acuminata is a favoured food of mobile frugivores such as Torres Strait pigeons and flying foxes. The decreased diversity with decreasing density of populations indicated that seed dispersal by frugivores has been important for the maintenance of diversity in this species. Populations known to have originated on relatively young, Holocene landforms were not necessarily genetically depauperate. Gene flow by pollen is apparently limited because C. acuminata populations are significantly inbred regardless of genetic diversity ( F = 0.641). The distribution and diversity of rare alleles, i.e. those occurring in few populations, is consistent with the theory of rainforest contraction during the Pleistocene.     

Genetic diversity in the endangered dysploid larkspur Delphinium bolosii and its close diploid relatives in the series Fissa of the Western Mediterranean area

Allozyme diversity was evaluated in four closely-related taxa of the Delphinium series Fissa distributed throughout the Western Mediterranean area. All are considered threatened plants. Delphinium bolosii and Delphinium mansanetianum are narrowly endemic to the Eastern Iberian Peninsula, whereas Delphinium fissum ssp. sordidum is found in a few populations across the Peninsula. Delphinium fissum ssp. fissum is more widely distributed but often in small and isolated populations. In this group, Delphinium bolosii is dysploid (2 n  = 18) whereas the other taxa are diploid (2 n  = 16). A total of 12 populations were surveyed, including all known locations for D. bolosii , D. mansanetianum , and D. fissum ssp. sordidum . Eleven enzyme systems were assayed and 15 loci were resolved. Markedly depauperate values for genetic diversity were obtained for D. mansanetianum ( H _e = 0.013) and D. fissum ssp. sordidum ( H _e = 0.044). The estimates for D. fissum ssp. fissum ( H _e = 0.071) were below the values expected for widespread species. Small population size and marginal distribution have probably contributed to the low variability observed in this group. By contrast, D. bolosii exhibited comparatively larger populations and greater genetic diversity ( H _e = 0.138). We suggest that, apart from population size and local adaptation, genetic diversity during speciation may have been promoted by dysploidy through genomic recombination.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 773–784.     

Exploring wild genetic resources of Musa acuminata Colla distributed in the humid forests of southern Western Ghats of peninsular India using ISSR markers

Musa acuminata ssp. burmannica, one of the wild progenitors contributing 'A genome' to the present-day dessert bananas, has a long evolutionary history intervened by human activities. In this study, ISSR markers were used to analyze the pattern of genetic variation and differentiation in 32 individuals along with two reference samples (viz., Musa acuminata ssp. burmannicoides, var. Calcutta 4 and Musa balbisiana) of wild Musa, which corresponded to three populations across the biodiversity-rich hot spot of southern Western Ghats of India. High levels of genetic diversity were revealed both at the species and population levels, using Nei's diversity indices. The hierarchical analysis of molecular variance showed pronounced genetic differentiation, as 96?% of the total variance was fixed within population and only 4?% among populations. Nei's genetic differentiation coefficient (G (ST)?=?0.1823) and low gene flow (Nm?=?1.18) further confirmed this. The positive correlation (Mantel test) between geographic distance and genetic distance (r?=?0.338 P?相似文献   

Phylogeography and host race differentiation in the European mistletoe (Viscum album L.)

Mistletoes are bird dispersed, hemi-parasitic shrubs infecting a large number of woody host plants. Chloroplast fragment length polymorphisms were used to study genetic differentiation among presumed host races, population genetic structure, and to elucidate the postglacial migration history of mistletoe ( Viscum album ) across the entire natural distribution range in Europe. The populations sampled belong to four closely related taxa, three of which are widely distributed and differ in their host trees, whereas a fourth taxon is rare and endemic to the Island of Crete. The molecular analysis of chloroplast DNA variation supported the distinction of these four taxa. We further found evidence for phylogeographical structure in each of the three widely distributed host races. Independent of host race, mistletoe haplotypes from Turkey were distinct and distant from those found elsewhere in Europe, suggesting that highly differentiated populations, and possibly new taxa, exist at the range limit of the species.     

Allozyme diversity in the endangered pitcher plant Sarracenia rubra ssp. Alabamensis (Sarraceniaceae) and its close relative S. rubra ssp. rubra

Genetic variability in the federally endangered pitcher plant Sarracenia rubra ssp. alabamensis was assessed in eight Alabama populations using starch gel electrophoresis. Ten populations of the more widespread Sarracenia rubra ssp. rubra were sampled in the southeastern United States for comparison. Fifteen allozyme loci representing 13 enzyme systems were scored for each species. In contrast to S. oreophila and S. jonesii, two previously analyzed endangered pitcher plants, genetic diversity was high for both S. rubra subspecies. Within ssp. alabamensis the percentage polymorphic loci (Ps) was 80.0, the mean number of alleles per polymorphic locus was (APs) = 2.58, and expected heterozygosity (Hes) was 0.209. Genetic diversity was slightly lower for ssp. rubra (Ps = 73.3, APs = 2.91, and Hes = 0.177). The proportion of total genetic diversity found among populations was fairly low for both species (GST = 0.09 for ssp. alabamensis and 0.14 for ssp. rubra). Little genetic divergence has occurred between the two subspecies as indicated by the lack of diagnostic alleles, the proportion of total genetic diversity between taxa (GST = 0.09), and the genetic identity estimate (I = 0.90). The relatively high genetic diversity found for ssp. alabamensis indicates that the maintenance of its evolutionary potential is possible if population sizes are maintained or increased. Low levels of genetic diversity found within small Georgia ssp. rubra populations indicate that genetic erosion may increase extinction risks for these populations.     

Patterns of genetic diversity in related taxa of Antirrhinum L. assessed using allozymes

Allozyme diversity was studied within and among populations of five related taxa of Antirrhinum L. endemic to the Iberian Peninsula ( A. graniticum Rothm. ssp. graniticum , ssp. brachycalyx Sutton and ssp. ambiguum (Lange) Mateu & Segarra, A. boissieri Rothm. and A. onubensis (Fdez. Casas) Fdez. Casas). All of the studied taxa are obligate outcrossing endemic perennial herbs which form isolated populations. However, the taxa vary in range and population sizes, and are found on different soil types. The level and distribution of allozyme diversity differed widely between taxa: A. graniticum ssp. brachycalyx had the lowest level of allozyme diversity (H_T = 0.09), whilst the highest level was detected in A. boissieri (H_T = 0.25). Total variation was partitioned into within- and among-population variation. The proportion attributable to variation within populations varied from about 67% up to 84.3% and 89.5% in A. graniticum ssp. brachycalyx and A. graniticum ssp. ambiguum , respectively. Both these subspecies also showed little population divergence (G_ST = 0.10 and 0.09, respectively) and had high levels of estimated gene flow (Nm = 2.18 and 2.62, respectively). These results are discussed in relation to geographical proximity of populations and habitat continuity. Isolation by distance was not detected in any of the studied taxa. This result suggests that divergence among populations is due to random genetic drift.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 79 , 299–307.     

Genetic diversity and structure of a rare endemic cactus and an assessment of its genetic relationship with a more common congener

Endemic, obligate outcrossing plant species with narrow geographic distributions and disjunct populations are prone to loss of genetic diversity. Simultaneously, delineating clear species boundaries is important for targeted conservation efforts. The rare and endemic cactus, Sclerocactus brevihamatus subsp. tobuschii (SBT), has a parapatric relationship with Sclerocactus brevihamatus subsp. brevihamatus (SBB) but genetic distance between the two taxa is unknown. We: (1) developed taxon-specific polymorphic microsatellites, (2) assessed genetic diversity within and among nine populations of SBT, and within one population of SBB, and (3) estimated the genetic relationship between the two subspecies. Within-population genetic diversity of SBT was moderate to high (mean H_o?=?0.37; mean H_e?=?0.59). Indirect estimate of inbreeding corrected for null alleles (F_is-INEst) was low for SBT, ranging from 0.03 to 0.14 (mean F_is-INEst?=?0.07). Genetic differentiation among populations of SBT was low based on F_st (0.08) and AMOVA (Ф_PT?=?0.10). Lack of genetic and spatial correlation in SBT populations coupled with the presence of private alleles and bottleneck events in several populations suggests that reproductive isolation is occurring but that sufficient time may not have yet passed to manifest strong differentiation. Cluster analyses segregated the 10 populations into three distinct groups, and separated SBB genotypes clearly. Results suggest that while hybridization between the two subspecies may occur, SBT is clearly differentiated genetically from SBB to retain its current taxonomic status.     

Genetic studies on Gadaba: a tribal population of Andhra Pradesh, India.

Blood samples were collected from Gadaba, a tribal population of Andhra Pradesh, South India, in order to examine the distribution of blood groups, red cell enzymes and the gammaglobulin polymorphism. Out of 20 genetic markers studied seven protein loci exhibited monomorphism. Surprisingly a case of a rare homozygous variant and twenty-one heterozygous variants at the phosphogluconate dehydrogenase locus (6-PGD), six variants at the phosphohexose isomerase locus (PHI) and a single case of phosphoglucomutase locus 1 (PGM 1) variant were observed. Further, the tribal populations of South India reveal higher frequencies of rare variants than the caste populations. However, the presence of rare variants that are phenotypically neutral may be plausibly due to their high selective value.     

Genetic diversity and differentiation processes in the ploidy series of Olea europaea L.: a multiscale approach from subspecies to insular populations

Geographical isolation and polyploidization are central concepts in plant evolution. The hierarchical organization of archipelagos in this study provides a framework for testing the evolutionary consequences for polyploid taxa and populations occurring in isolation. Using amplified fragment length polymorphism and simple sequence repeat markers, we determined the genetic diversity and differentiation patterns at three levels of geographical isolation in Olea europaea : mainland-archipelagos, islands within an archipelago, and populations within an island. At the subspecies scale, the hexaploid ssp. maroccana (southwest Morocco) exhibited higher genetic diversity than the insular counterparts. In contrast, the tetraploid ssp. cerasiformis (Madeira) displayed values similar to those obtained for the diploid ssp. guanchica (Canary Islands). Geographical isolation was associated with a high genetic differentiation at this scale. In the Canarian archipelago, the stepping-stone model of differentiation suggested in a previous study was partially supported. Within the western lineage, an east-to-west differentiation pattern was confirmed. Conversely, the easternmost populations were more related to the mainland ssp. europaea than to the western guanchica lineage. Genetic diversity across the Canarian archipelago was significantly correlated with the date of the last volcanic activity in the area/island where each population occurs. At the island scale, this pattern was not confirmed in older islands (Tenerife and Madeira), where populations were genetically homogeneous. In contrast, founder effects resulted in low genetic diversity and marked genetic differentiation among populations of the youngest island, La Palma.     

Genetic diversity and multilocus genetic structure in the relictual endemic herb<Emphasis Type="Italic"> Japonolirion osense</Emphasis> (Petrosaviaceae)

Plant clonality may greatly reduce effective population size and influence management strategies of rare and endangered species. We examined genetic diversity and the extent of clonality in four populations of the monotypic herbaceous perennial Japonolirion osense, which is one of the most rare flowering plants in Japan. Allozyme analysis revealed moderate levels of genetic variation, and the proportion of polymorphic loci (P=66.7%) was higher than the value for species with similar life-history traits. With four polymorphic loci, 19 multilocus genotypes were observed among 433 aerial shoot samples and 10 (52%) were found only in single populations. The proportion of distinguishable genotypes (PD=0.10) and Simpson's index of diversity (D=0.52) also exhibited moderate levels of genotypic diversity compared to other clonal plants, with genotype frequencies at Hardy-Weinberg equilibrium. The distributions of genotypes were often localized and they were mostly found within a radius of 5 m. Spatial autocorrelation analysis showed that shoot samples located 4 m apart were expected to be genetically independent. The results suggest that the spatial extent of genets was relatively narrow and thus the clonality was not extensive.     

Speciation and domestication in maize and its wild relatives: evidence from the globulin-1 gene.

The grass genus Zea contains the domesticate maize and several wild taxa indigenous to Central and South America. Here we study the genetic consequences of speciation and domestication in this group by sampling DNA sequences from four taxa-maize (Zea mays ssp. mays), its wild progenitor (Z. mays ssp. parviglumis), a more distant species within the genus (Z. luxurians), and a representative of the sister genus (Tripsacum dactyloides). We sampled a total of 26 sequences from the glb1 locus, which encodes a nonessential seed storage protein. Within the Zea taxa sampled, the progenitor to maize contains the most sequence diversity. Maize contains 60% of the level of genetic diversity of its progenitor, and Z. luxurians contains even less diversity (32% of the level of diversity of Z. mays ssp. parviglumis). Sequence variation within the glb1 locus is consistent with neutral evolution in all four taxa. The glb1 data were combined with adh1 data from a previous study to make inferences about the population genetic histories of these taxa. Comparisons of sequence data between the two morphologically similar wild Zea taxa indicate that the species diverged approximately 700, 000 years ago from a common ancestor of intermediate size to their present populations. Conversely, the domestication of maize was a recent event that could have been based on a very small number of founding individuals. Maize retained a substantial proportion of the genetic variation of its progenitor through this founder event, but diverged rapidly in morphology.     

Woody climbers show greater population genetic differentiation than trees: Insights into the link between ecological traits and diversification

The climbing habit is a key innovation in plants: climbing taxa have higher species richness than nonclimbing sister groups. We evaluated the hypothesis that climbing plant species show greater among‐population genetic differentiation than nonclimber species. We compared the among‐population genetic distance in woody climbers (eight species, 30 populations) and trees (seven species, 29 populations) coexisting in nine communities in a temperate rainforest. We also compared within‐population genetic diversity in co‐occurring woody climbers and trees in two communities. Mean genetic distance between populations of climbers was twice that of trees. Isolation by distance (increase in genetic distance with geographic distance) was greater for climbers. Climbers and trees showed similar within‐population genetic diversity. Our longevity estimate suggested that climbers had shorter generation times, while other biological features often associated with diversification (dispersal and pollination syndromes, mating system, size, and metabolic rate) did not show significant differences between groups. We hypothesize that the greater population differentiation in climbers could result from greater evolutionary responses to local selection acting on initially higher within‐population genetic diversity, which could be driven by neutral processes associated with shorter generation times. Increased population genetic differentiation could be incorporated as another line of evidence when testing for key innovations.     

Ancient DNA and conservation: lessons from the endangered kiwi of New Zealand

Conservation genetics typically seeks to map the distribution of contemporary genetic variation across space, and to use the resulting genetic parameters to infer any likely short-term evolutionary consequences for rare and endangered species. Recent developments in the study of ancient DNA now enable the extension of genetic variation studies backwards in time and provide a context by which to interpret contemporary levels of genetic variation, in addition to any patterns of genetic change over time. Ancient DNA research can also help to determine past levels of genetic diversity, identify species' boundaries and reveal former ranges among morphologically cryptic taxa. Ancient DNA sequence data for the New Zealand kiwi (Apteryx spp.) are presented and we show that most ancient populations of rowi and tokoeka exhibited private mitochondrial DNA haplotypes. Moreover, we illustrate that the extinction of these populations has led to the loss of considerable genetic variation. We also use ancient DNA methodology to determine past species distributions for brown kiwi and great spotted kiwi whose bones are morphologically indistinguishable.     

Ice ages leave genetic diversity ‘hotspots’ in Europe but not in Eastern North America

After the last glacial cycle, temperate European trees migrated northward, experiencing genetic bottlenecks and founder effects, which left high haplotype endemism in southern populations and clines in genetic diversity northward. These patterns are thought to be ubiquitous across temperate forests, and are therefore used to anticipate the potential genetic consequences of future warming. We compared existing and new phylogeographic data sets (chloroplast DNA) from 14 woody taxa in Eastern North America (ENA) to data sets from 21 ecologically similar European species to test for common impacts of Quaternary climate swings on genetic diversity across diverse taxa and between continents. Unlike their European counterparts, ENA taxa do not share common southern centres of haplotype endemism and they generally maintain high genetic diversity even at their northern range limits. Differences between the genetic impacts of Quaternary climate cycles across continents suggest refined lessons for managing genetic diversity in today's warming world.     

Genetic diversity and differentiation of allopolyploid Dactylorhiza (Orchidaceae) with particular focus on the Dactylorhiza majalis ssp. traunsteineri/lapponica complex

Genetic differentiation of Dactylorhiza majalis ssp. traunsteineri from the Alps, Scandinavia, and Britain was studied and compared with other allotetraploid members of the systematically challenging genus Dactylorhiza . One-hundred and eleven populations from altogether 18 taxa were analysed for eight polymorphic plastid markers and two size-variable fragments from the nuclear internal transcribed spacer (ITS) region. In total, 60 plastid haplotypes and six ITS alleles were found among the 737 individuals analysed. No clear differentiation between populations of ssp. traunsteineri from the three regions was revealed. However, ssp. traunsteineri was genetically differentiated from Dactylorhiza baumanniana , Dactylorhiza elata , and D. majalis ssp. sphagnicola , although the majority of allotetraploid taxa remained inseparable. Judging from the degree of concerted evolution in ITS, D. majalis ssp. alpestris may be regarded as a relatively old allotetraploid, whereas ssp. baltica and ssp. purpurella may be considerably younger. Based on plastid data, the Alp region had the highest genetic diversity followed by Scandinavia and Britain. The geographic distribution of haplotypes provided support for possible refugial areas around the Alps and for several independent immigration routes into Scandinavia after the last ice age.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 52–67.     

Characterization of polymorphic microsatellite DNA markers in Hakea oldfieldii Benth. (Proteaceae)

A genomic library was constructed and 13 polymorphic microsatellite markers were developed for Hakea oldfieldii, a woody shrub endemic to southwest Western Australia. Polymorphism was investigated for these markers in 28 individuals from a single population located in restricted habitat at the base of the Whicher Range south of Busselton. Expected heterozygosity ranged from 0.279 to 0.770 and averaged 0.633. Observed heterozygosity ranged from 0.321 to 0.786 and averaged 0.598. The number of alleles per locus ranged from 2.0 to 6.0 and averaged 4.5. These markers will be used to assay genetic diversity and pollen dispersal in this species.     

Molecular Genetic Variation in Chinese Populations of Three Subspecies of Hippophae rhamnoides

To provide a population-level genetic profile for investigation and conservation of genetic diversity of the sea buckthorn (Hippophae rhamnoides L.), 300 individuals of fifteen natural populations of sea buckthorn in China were analyzed by using ISSR (inter-simple sequence repeats) markers. On the basis of Shannon's index and Nei's genetic diversity, the mean genetic diversity detected in the natural populations of Hippophae rhamnoides ssp. yunnanensis, ssp. sinensis, and ssp. gyantsensis was 0.1944, 0.2169, and 0.1372, respectively. The coefficient of gene differentiation (Gst) of seven ssp. yunnanensis populations is 0.2790, and that of seven ssp. sinensis populations is 0.4184. This means that 28% of the total molecular variance of seven ssp. yunnanensis populations existed among populations, and 42% for seven ssp. sinensis populations, suggesting that the subspecies have different genetic structures. No significant correlation between genetic and geographic distances of the populations was found using ISSR markers.     

Evolutionary patterns and genetic structure in localized and widespread species in the Stylidium caricifolium complex (Stylidiaceae)

The Stylidium caricifolium (Stylidiaceae) complex consists of seven currently recognized species and a taxon of putative hybrid origin endemic to southwest Western Australia. These taxa vary in geographical distribution from widespread, extending over a range of 500 km, to extremely localized, covering a range of only 0.5 km. Patterns of allozyme variation were investigated in 61 populations covering all taxa and two closely related species. Measures of genetic diversity were consistently lower and in some cases significantly lower in four rare and geographically restricted taxa compared with their widespread relatives. In contrast, genetic diversity in two other localized taxa was comparable or higher than in the widespread taxa. The level of divergence among populations was moderate to high, with a significant trend of higher F(ST) values for the widespread species to lower values for the geographically restricted and rare taxa. Phylogenetic relationships and levels of divergence indicate that most taxa are probably relictual rather than recently evolved. Geographical localization and rarity in this complex can be attributed to a range of factors associated with habitat specificity, historical and ecological processes that characterize the southwest region, and mode of origin.     

Genetic Variation Within and Among Metal-Tolerant and Non-Tolerant Populations of Armeria maritima (Mill.) Willd. s.l. (Plumbaginaceae) in Central and Northeast Germany

Abstract: Six metal-tolerant populations and sub-populations of Armeria maritima ssp. halleri, ssp. hornburgensis, and ssp. bottendorfensis and two non-tolerant populations of ssp. elongata in Central and Northeast Germany have been analysed using RAPD markers. The populations show very strong genetic differentiation (Φ_ST = 0.46), corresponding gene flow between them is low (N_em = 0.29). A moderate positive correlation between the matrices of genetic and geographical distances was found between the seven populations and sub-populations of central Germany (r = 0.68, p < 0.001). Calculated parameters of genetic variability are molecular variance, percentage of heterozygosity and percentage of polymorphic loci. A significant correlation between population size and parameters of genetic variability was not recognisable. Genetic structure was investigated by an analysis of molecular variance (AMOVA). The studied populations show strong genetic differentiation. Genetic variation within populations ("normal" as well as metalliferous) is higher (53.9 %) than among them (46.1 %). Six hypotheses of possible genetic relatedness between the studied populations have been tested by AMOVA. A data set structure above the populational level is hardly recognisable. It was impossible to combine the populations to edaphic (tolerant and "non-tolerant") or taxonomic groups. A. maritima ssp. halleri of the north Harz mountains and ssp. hornburgensis are clearly separated from a geographical group containing all other populations (across taxonomic and edaphic boundaries). These results are a further indication for a polyphyletic origin of metal-tolerant populations of A. maritima s.l. by multiple colonizations of metalliferous sites from neighbouring populations on non-metalliferous soil.