Amplified Fragment Length Polymorphism Data Research Articles

Genetic variability of Beauveria bassiana and Metarhizium anisopliae var. anisopliae isolates obtained from the Eastern Black Sea Region of Turkey

Beauveria bassiana (Balsamo) Vuillemin and Metarhizium anisopliae var. anisopliae (Metschnikoff) Sorokin are the most common entomopathogenic fungi used in microbial control programs all over the world. Assessments of the genetic variability of these 2 important species are useful for the development of effective biocontrol strategies and for evaluating the impact of artificial epizootics. In this study, the genetic diversity of 13 B. bassiana and 33 M. anisopliae var. anisopliae strains isolated from the hazelnut-growing region of Turkey was determined by using the amplified fragment length polymorphism (AFLP) and \alpha- and \beta-isoenzyme analyses. Cluster analysis of AFLP data clearly separated both B. bassiana and M. anisopliae var. anisopliae strains into 3 and 4 different groups, respectively. While \alpha- and \beta-esterase banding patterns clearly separated M. anisopliae var. anisopliae strains, it did not give enough information about B. bassiana strains. We also assessed the growing ability of all isolates at different temperatures (8, 16, 25, and 37 °C) and UV exposures (30 and 60 min), and virulence against Tenebrio molitor. These results indicated that there is a significant variability within the B. bassiana and M. anisopliae var. anisopliae populations in this region. Although the diversity of B. bassiana isolates is associated with geographic location, it is not associated with habitat type. There is also no association amongst B. bassiana isolates in terms of the ability to grow at different temperatures and UV exposures, or virulence against T. molitor. The diversity of M. anisopliae var. anisopliae strains is neither associated with habitat type nor geographic location, and there is no association amongst M. anisopliae var. anisopliae strains in terms of the ability to grow at different temperatures (except for 16 °C) and UV exposure, or virulence against T. molitor. The data presented here might be useful for controlling some hazelnut pests in this region.

Ranunculus ×prieti (Ranunculaceae): A new hybrid from the Cantabrian Mountains (North of Spain) revealed by morphological and molecular analyses

A new nothospecies Ranunculus ×prieti is described following morphological and molecular characterization. Hypervariable Amplified Fragment Length Polymorphism (AFLP) markers, flow cytometry (FCM) analysis and pollen viability were conducted. The profiles of hybrid samples were compared to their presumed parental taxa R. amplexicaulis and R. gramineus. Morphological study revealed that all hybrid individuals were morphologically intermediate between their parents, showing ovate-lanceolate basal leaves and amplexicaul cauline leaves as in R. amplexicaulis and yellow corollas as in R. gramineus. Principal coordinates analysis of the AFLP data set showed that hybrids are closer to R. gramineus than to R. amplexicaulis, whereas the results obtained by flow cytometry indicate otherwise. Pollen fertility estimation of R. ×prieti ranged from 68.83 to 95.81%, showing that hybrid samples are well established and fertile.

Ecological associations and genetic divergence in Black-bellied Salamanders (Desmognathus quadramaculatus) of the Southern Appalachian Mountains

th October. Abstract. The discovery and subsequent description of cryptic biodiversity is often chal- lenging, especially for groups that have undergone rapid lineage accumulation in the relatively recent past. Even without formal descriptions, understanding genetic diversity patterns as they relate to underlying ecological or historical processes can be important for conservation. The dusky salamanders of the genus Desmognathus, with 20 described species, comprise the second largest genus of plethodontid salamanders in the eastern United States. However, due to the presence of high genetic diversity and relatively few morphological synapomorphies, the number of species is likely to increase. For the three nominal species within the D. quadramaculatus species complex, including D. quad - ramaculatus, D. folkertsi, and D. marmoratus, we used a portion of the mitochondrial genome and nuclear markers in the form of amplified fragment length polymorphisms (AFLP) to uncover spatial patterns of genetic diversity. Within D. quadramaculatus and D. marmoratus, we uncovered four well-supported lineages with the mitochondrial sequences; phylogeographic patterns were not congruent with the AFLP data. Both sets of markers identified a clear isolation by stream distance. Using multiple regressions, we found that historical river drainages and terrestrial ecoregions explained the phylogeo- graphic patterning we observed for D. quadramaculatus .

Genetic diversity in NaN3-induced common bean mutants and commercial varieties detected by AFLP

The analysis of Amplified Fragment Length Polymorphism (AFLP) was used to estimate genetic diversity in common bean (Phaseolus vulgaris L.) variety Hwachia and in 34 NaN3-induced mutants and 11 commercial varieties introduced from China. Eight primer combinations generated 516 DNA fragments of the tested mutants and introduced varieties, of which 448 fragments were polymorphic. The calculated Jaccard similarity coefficients based on AFLP data ranged from 0.47 to 0.84. The molecular profiles obtained from eight AFLP primer pairs indicated a high genetic diversity among Hwachia, NaN3-induced mutants and introduced varieties. The extent of genetic variation was slightly higher between Hwachia and NaN3-induced mutants than between Hwachia and introduced commercial varieties. These results, supported by cluster analysis, suggest that NaN3-induced mutagenesis effectively broadens the genetic diversity of common bean varieties. Some of the produced mutants could be useful as sources of variation to develop new improved common bean varieties.

Ancient Hybridization and Phenotypic Novelty within Lake Malawi's Cichlid Fish Radiation

Does hybridization play a broad innovative role in evolution? Many studies have shown hybrid origins of individual species, particularly in major adaptive radiations, but this may be a consequence, rather than a cause, of the existence of many closely related species. Cases of hybridization in the early stages of major adaptive radiations are comparatively rare. Here, we report phylogenetic evidence for ancient introgression between distinct lineages of the species-rich Lake Malawi haplochromine cichlid fishes. Mitochondrial DNA (mtDNA) sequences indicated surprisingly close relationships between the shallow-water rocky habitat "Mbuna" species and a group of dark-adapted "Deep-Benthic" species specialized for feeding in low-light conditions (dawn/dusk, under overhangs, and deep water). By contrast, analyses of nuclear amplified fragment length polymorphism data demonstrated that these Deep-Benthic cichlids were more closely related to shallow water "Shallow-Benthic" soft-sediment feeders, a group that shares similar head and body morphology. A coalescent-based computer simulation indicated that the mtDNA similarity of rocky habitat Mbuna species and dark-adapted Deep-Benthic species was due to hybridization rather than incomplete lineage sorting. Comparisons of morphology indicated that some Deep-Benthic species possessed novel morphology not present in other Lake Malawi species groups. Thus, these analyses support the hypothesis that ancient hybridization occurred within the Lake Malawi cichlid radiation, that the event occurred before the radiation of a species group adapted to low-light benthic habitats, and that this group went on to dominate the deep-water regions of Lake Malawi. The results of this study contribute to a growing literature consistent with a creative role of hybridization in the evolution of species diversity and adaptive radiations.

Morphological and AFLP diversity in Thaumatococcus daniellii, the source of the protein sweetener thaumatin

Thaumatococcus daniellii is a perennial African wild edible plant. Fruit arils from natural populations are the source of the protein sweetener, thaumatin. There are relatively few documented examples of its cultivation, however it has great potential as an intercrop for cultivation under rubber or cocoa. Across the species range there is notable diversity in leaf and fruit morphology. In this study, T. daniellii populations from four provenances in Ghana and Cameroon (separated by the Dahomey Gap) were compared for leaf and fruit morphology in situ and in an experiment using plants grown from sampled rhizomes planted under rubber in a single location in Cameroon. When collected rhizomes from four provenances were planted at one location, the samples from the local provenance produced the largest plants and fruits, and there was less morphological variation between samples from different provenances than was recorded in situ. In situ morphological differences were notable between north–south separated provenances in each country. Fruit collected in situ was analysed for aril thaumatin content and significant variation was found between provenances (1.08–2.00%). Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity among the four provenances and 54% of loci were polymorphic. Cluster analysis of AFLP data separated samples of T. daniellii according to geographical origin. Maximum genetic diversity was found between provenances separated across the Dahomey Gap.

Conservation genetics of the critically endangered Round Island bottle palm, Hyophorbe lagenicaulis (Arecaceae): can cultivated stocks supplement a residual wild population?

The amplified fragment length polymorphism (AFLP) technique was used to examine genetic variation among old and newly emerged individuals of Hyophorbe lagenicaulis (the Round Island bottle palm) on Round Island to assess surviving levels of diversity in the wild population and to evaluate the suitability of old cultivated stocks on Mauritius as a source of seed for reintroduction. The analysis of AFLP data for 48 individuals of H. lagenicaulis (individuals from Round Island and elsewhere), two H. verschaffeltii, two H. vaughanii, one H. amaricaulis and one H. indica yielded 81 variable and six monomorphic bands. Analysis of molecular variance (AMOVA) and Shannon's indices showed a high level of genetic variation within the wild population on Round Island and a smaller amount of genetic variation among cultivated individuals. A neighbor joining analysis resulted in an unrooted network of genetic distances in which the five Hyophorbe spp. were separated and much variation within H. lagenicaulis was recovered. The Round Island populations of H. lagenicaulis contain representatives of the genetic variation found within the species as a whole. However, a few individuals, both wild and cultivated, represent apparently rare AFLP profiles, and thus, if a more representative distribution of genotypes is wanted for the wild population, cultivated sources could be introduced to Round Island from Mauritian gardens and plantings. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167, 301–310.

Landscape and climatic effects on the evolutionary diversification of the Perognathus fasciatus species group

We evaluated evolutionary relationships of taxa within silky pocket mice of the Perognathus fasciatus species group, composed of 3 species, P. fasciatus, P. flavescens, and P. apache. These species are distributed throughout the Great Plains, Wyoming Basin, Colorado Plateau, and northern Chihuahuan Desert biogeographic regions in North America. We tested a previously postulated hypothesis of Pleistocene species divergence and introgression by analyzing mitochondrial DNA (mtDNA) and amplified fragment length polymorphisms (AFLPs). Both mtDNA and AFLP data support several genetic lineages in the fasciatus species group that are geographically structured. Molecular clock estimates reject a Pleistocene speciation hypothesis in favor of a deeper, more complex evolutionary history of initial divergence in the Miocene followed by secondary diversification beginning in the middle Pliocene and progressing through the Pleistocene. Results support recognition of an additional species within the group. Temporal and spatial congruence between the mtDNA clades in the fasciatus species group and other codistributed species of Perognathus appear to support a hypothesis of concerted diversification throughout the Chihuahuan Desert, Colorado Plateau, and Great Plains.

English

The population structure of Japanese flounder (Paralichthys olivaceus) in the Yellow and East China Seas were analyzed using amplified fragment length polymorphism (AFLP) and cytochrome c oxidase subunit I (COI) gene sequencing. A total of 390 reproducible bands were generated by 10 AFLP primer combinations in two populations collected from the coasts of Qingdao (located at the Yellow Sea) and Zhoushan (located at the East China Sea). The percentage of polymorphic loci (P), Nei’s genetic diversity (H) and Shannon’s information index (I) values were higher in the Qingdao population (P = 72.85%, H = 0.243 and I = 0.364) than those in the Zhoushan population (P = 56.35%, H = 0.189 and I = 0.284). The genetic diversity reduction in the Zhoushan population may be attributed to fishing pressure and habitat loss in this area. Based on the COI sequencing analysis, a total of 25 polymorphic sites were examined, and 15 haplotypes were identified in the two populations. The haplotype diversity (h) and nucleotide diversity (π) values in the Qingdao population were 0.746 ± 0.0728 and 0.00334 ± 0.00103, respectively. The corresponding values in the Zhoushan population were 0.712 ± 0.0470 and 0.00318 ± 0.00049. Both the AFLP and mtDNA data revealed significant genetic differentiation between the two populations. The present study discussed the factors that may result in genetic differentiation between the populations in the Yellow and East China Seas.   Keywords: Japanese flounder, amplified fragment length polymorphism (AFLP), cytochrome c oxidase subunit I (COI) gene, genetic diversity, population structure.

Resolution of the Acanthopagrus black seabream complex based on mitochondrial and amplified fragment‐length polymorphism analyses

In this study, DNA analyses were employed to verify the identity of six morphologically similar species that occur in the coastal waters of Taiwan: the black seabream complex (Acanthopagrus latus, Acanthopagrus schlegelii, Acanthopagrus sivicolus, Acanthopagrus taiwanensis, Acanthopagrus chinshira and Acanthopagrus pacificus). Amplified fragment-length polymorphism (AFLP) analyses clearly distinguished the same six species that are morphologically diagnosable based on subtle differences in scale counts and anal-fin colouration. In contrast, mitochondrial DNA analyses based on cytochrome b gene sequences did not distinguish individuals of A. schlegelii and A. sivicolus, reflecting either historical introgression or recent speciation and incomplete sorting of their mitochondrial lineages. Phylogenetic relationships among these six north-west Pacific Ocean species of Acanthopagrus analysed using AFLP data were consistent with scale rows above the lateral line (TRac), sperm ultrastructure and geographical distribution. The study provides molecular tools for future research relevant to improved management of these resources, and an increased understanding of the evolutionary history of this radiation.

Hybridization and asymmetric introgression between Cypripedium tibeticum and C. yunnanense in Shangrila County, Yunnan Province, China

Hybridization and introgression are thought to be important for speciation and adaptation in many plants. However, little is known about the hybridization and introgression among Cypripedium species. To investigate the evidence for hybridization and the pattern of introgression between Cypripedium yunnanense and C. tibeticum in Shangrila County, Yunnan Province, China, morphological characters and amplified fragment length polymorphism (AFLP) data for both the species and their putative hybrids were studied. Hand pollination was also performed to verify the crossability of the putative parents. Principal coordinate analysis based on morphological characters and the AFLP data suggested that the putative hybrids were true hybrids of these two Cypripedium species. Analysis with the NewHybrids software indicated that the putative hybrids were F1 generation individuals and backcrosses to C. yunnanese, but no F2 generation was found. Analysis with the Structure software demonstrated asymmetric introgression from C. tibeticum to C. yunnanense. We conclude that natural hybridization and introgression can occur between these two species and that in situ conservation of the parental species is required before fully assessing the evolutionary potential of hybrids.

Salmonella enterica in Swine Production: Assessing the Association between Amplified Fragment Length Polymorphism and Epidemiological Units of Concern

The aims of this study were to determine the ability of amplified fragment length polymorphism (AFLP) to differentiate Salmonella isolates from different units of swine production and to demonstrate the relatedness of Salmonella between farms and abattoirs by AFLP. Twenty-four farms in the midwestern United States were visited four times from 2006 to 2009. At each farm or abattoir visit, 30 fecal samples or 30 mesenteric lymph nodes were collected, respectively. A total of 220 Salmonella isolates were obtained, serotyped, and genotyped by multilocus sequence typing (MLST) and AFLP. These 220 isolates clustered into 21 serotypes, 18 MLST types, and 14 predominant AFLP clusters based on a genetic similarity threshold level of 60%. To assess genetic differentiation between farms, harvest cohorts, and pigs, analysis of molecular variance was conducted using AFLP data. The results showed 65.62% of overall genetic variation was attributed to variance among pigs, 27.21% to farms, and 7.17% to harvest cohorts. Variance components at the farm (P = 0.003) and pig (P = 0.001) levels were significant, but not at the harvest cohort level (P = 0.079). A second analysis, a permutation test using AFLP data, indicated that on-farm and at-abattoir Salmonella from pigs of the same farms were more related than from different farms. Therefore, among the three subtyping methods, serotyping, MLST, and AFLP, AFLP was the method that was able to differentiate among Salmonella isolates from different farms and link contamination at the abattoir to the farm of origin.

Molecular characterization of intra-population variability of Jatropha curcas L. using DNA based molecular markers

Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity of J. curcas germplasm. In the present study, efforts were made to analyze the genetic diversity among the elite germplasms of J. curcas, selected on the basis of their performance in field using random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR). The plants were selected on the basis of height, canopy circumference, number of seeds per fruit, weight of 100 seeds, seed yield in grams per plant and oil content. Out of 250 RAPD (with 26 primers), 822 AFLP (with 17 primers) and 19 SSR band classes, 141, 346 and 7 were found to be polymorphic, respectively. The percentage polymorphism among the selected germplasms using RAPD, AFLP and SSR was found to be 56.43, 57.9, and 36.84, respectively. The Jaccard's similarity coefficient was found 0.91, 0.90 and 0.91 through RAPD, AFLP and SSR marker systems, respectively. Principle component analysis (PCA) and dendrogarm analysis of genetic relationship among the germplasm using RAPD, AFLP and SSR data showed a good correlation for individual markers. The germplasm JCC-11, 12, 13, 14 and 15 whose yield found to be high were clustered together in dendrogram and PCA analysis though JCC11 is geographically distinct from others. In overall analysis JCC6 (in RAPD), JCC8 (in AFLP) and JCC 6 and JCC10 (in SSR) were found genetically diverse. Characterization of geographically distinct and genetically diverse germplasms with varied yield characters is an important step in marker assisted selection (MAS) and it can be useful for breeding programs and QTL mapping.

Evidence for progenitor–derivative speciation in sexually deceptive orchids

Sexually deceptive orchids of the genus Ophrys use mimicry of pollinator females to attract specific pollinators. Pollinator shifts may drive speciation in Ophrys, since novel pollinators may in principle act as isolating factors immediately. It is thus possible that evolution of novel species occurs rapidly and with a progenitor-derivative pattern. The aims of this study are to compare genetic structure and diversity among widespread and geographically restricted Ophrys taxa, to test whether genetic structure is associated with specific pollinators, and to investigate whether any widespread species may have acted as a progenitor for the evolution of more restricted taxa. Genetic differentiation and diversity were investigated in O. leucadica and O. cinereophila, the two taxa of the Ophrys fusca sensu lato complex widespread in the Aegean, and three geographically restricted taxa from Rhodes, O. attaviria, O. parvula and O. persephonae, all differing in their specific pollinators. This was done using amplified fragment length polymorphism (AFLP) DNA fingerprinting, and sequencing of the low-copy nuclear gene LEAFY (LFY). All taxa were found to be separate genetic entities, with O. leucadica forming two geographic groups from the west and east of the Aegean. Genetic structure was significantly shaped by pollinators and geography, and comparison of sequence and AFLP data revealed ancestral polymorphisms shared among several taxa. Among the sampled taxa, O. leucadica harbours the greatest genetic differentiation and geographic structure, and the highest genetic diversity. Part of the genome of O. parvula, endemic to Rhodes, may be derived from O. leucadica. Pollinators probably influence the genetic structure of the investigated Ophrys species. The genetic pattern identified is consistent with O. leucadica being the oldest of the sampled taxa, making O. leucadica a candidate progenitor species from which more restricted taxa such as O. parvula may have evolved.

The relative contribution of band number to phylogenetic accuracy in AFLP data sets

We examined the effect of increasing the number of sampled amplified fragment length polymorphism (AFLP) bands to reconstruct an accurate and well-supported AFLP-based phylogeny. In silico AFLP was performed using simulated DNA sequences evolving along balanced and unbalanced model trees with recent, uniform and ancient radiations and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.05 substitutions per site. Trees were estimated by minimum evolution (ME) and maximum parsimony (MP) methods from both DNA sequences and virtual AFLP fingerprints. The comparison of the true tree with the estimated AFLP trees suggests that moderate numbers of AFLP bands are necessary to recover the correct topology with high bootstrap support values (i.e. >70%). Fewer numbers of bands are necessary for shorter tree lengths and for balanced than for unbalanced tree topologies. However, branch length estimation was rather unreliable and did not improve substantially after a certain number of bands were sampled. These results hold for different levels of genome coverage and number of taxa analysed. In silico AFLP using bacterial genomic DNA sequences recovered a well-supported tree topology that mirrored an empirical phylogeny based on a set of 31 orthologous gene sequences when as few as 263 AFLP bands were scored. These results suggest that AFLPs may be an efficient alternative to traditional DNA sequencing for accurate topology reconstruction of shallow trees when not very short ancestral branches exist.

Amplified fragment length polymorphisms (AFLPs) analysis of species of Solanum section Solanum (Solanaceae ) from Uganda

The taxonomy of species belonging to Solanum section Solanum (sometimes referred to as the Solanum nigrum complex or black nightshades) is known to be difficult and has resulted in extensive synonymy. Yet, these species play a significant role in nutrition and food security, especially in developing countries. The amplified fragment length polymorphisms (AFLPs) technique was used to assess the genetic relationships among 107 accessions representing eight species of the section Solanum and to obtain new insight into the taxonomic status of the S. nigrum complex. Four primer combinations yielded 510 AFLP bands, only 29 of which were monomorphic. Neighbor-joining and principal coordinates analyses were performed. The AFLP data only partially correlated with earlier classifications based on morphology. We have been able to confirm the presence of only 5 out of eight species of this complex previously recognized from Uganda, that is, Solanum americanum, Solanum scabrum, Solanum hirsutum, Solanum florulentum/Solanum tarderemotum and Solanum villosum . In addition, S. villosum did not separate in accordance with previous subspecific ranks. It is likely that neither Solanum grossidentatum, S. nigrum nor Solanum sarrachoides occurred in Uganda. Also, there was no correlation between geographic localities for the Ugandan material and the AFLP results, indicating that most of the studied species are introduced. Key words: Amplified fragment length polymorphisms (AFLPs), Solanum nigum complex, Africa, genetic variation, taxonomy, Uganda.

Karyotype and AFLP data reveal the phylogenetic position of the Brazilian endemic Hypochaeris catharinensis (Asteraceae)

The genus Hypochaeris offers an excellent model for studies of recent adaptive radiation in the South American continent. We used karyotype analysis with chromomycin A3 (CMA3)/4’,6-diamidino-2-phenylindole (DAPI) banding and fluorescence in situ hybridization (FISH), and amplified fragment length polymorphism (AFLP) fingerprinting to investigate for the first time the Brazilian endemic H. catharinensis and define its position within the South American group of species. Strong CMA-positive signals were seen at the end of both arms of chromosome 3 and at the end of the long arm of chromosome 4. DAPI bands were only detected in subterminal position on short arm of chromosome 4. FISH with 5S and 35S ribosomal DNA (rDNA) probes revealed a single 5S rDNA locus on short arm of chromosome 2, typical for all other South American Hypochaeris taxa analyzed to date. The 35S rDNA locus was identified at subterminal position on the short arm of chromosome 3, as reported so far for only two of the known species (H. lutea and H. patagonica). The AFLP study included 55 individuals, comprising nine species of the South American Hypochaeris plus their putative ancestor H. angustifolia. Eleven AFLP primer combinations generated a total of 401 fragments, of which 388 (96.7%) were polymorphic. High genetic similarities were observed among taxa, with all South American Hypochaeris species falling into one main cluster [100% bootstrap (BS)]. Hypochaeris catharinensis is closely related to H. lutea (82% BS), forming a well-separated subcluster within the South American species. Taken together, the karyological and AFLP data contribute to the placement of H. catharinensis within the phylogenetic framework of South American species of Hypochaeris and allow the definition of a novel and well-resolved phylogenetic group (the Lutea group).

Increased inbreeding and strong kinship structure in Taxus baccata estimated from both AFLP and SSR data

Habitat fragmentation can have severe genetic consequences for trees, such as increased inbreeding and decreased effective population size. In effect, local populations suffer from reduction of genetic variation, and thus loss of adaptive capacity, which consequently increases their risk of extinction. In Europe, Taxus baccata is among a number of tree species experiencing strong habitat fragmentation. However, there is little empirical data on the population genetic consequences of fragmentation for this species. This study aimed to characterize local genetic structure in two natural remnants of English yew in Poland based on both amplified fragment length polymorphism (AFLP) and microsatellite (SSR) markers. We introduced a Bayesian approach that estimates the average inbreeding coefficient using AFLP (dominant) markers. Results showed that, in spite of high dispersal potential (bird-mediated seed dispersal and wind-mediated pollen dispersal), English yew populations show strong kinship structure, with a spatial extent of 50-100 m, depending on the population. The estimated inbreeding levels ranged from 0.016 to 0.063, depending on the population and marker used. Several patterns were evident: (1) AFLP markers showed stronger kinship structure than SSRs; (2) AFLP markers provided higher inbreeding estimates than SSRs; and (3) kinship structure and inbreeding were more pronounced in denser populations regardless of the marker used. Our results suggest that, because both kinship structure and (bi-parental) inbreeding exist in populations of English yew, gene dispersal can be fairly limited in this species. Furthermore, at a local scale, gene dispersal intensity can be more limited in a dense population.

OptiFLP: software for automated optimization of amplified fragment length polymorphism scoring parameters

Amplified fragment length polymorphism (AFLP), a widely used method for DNA fingerprinting, has shifted from polyacrylamide gel to capillary electrophoresis over the last years. Currently, most AFLP data are generated in a computer-readable format, and several programs are available that automatically score raw data into binary profiles. Good scoring parameters are the key to good AFLP profiles. optiFLP is the first open source program for automatic optimization of AFLP scoring parameters. It searches parameter space to maximize the contrast among groups of AFLP profiles, with the allocation of profiles to groups in either a supervised or an unsupervised mode. The software produces output files ready for use in a range of downstream applications.

Ecology and life history affect different aspects of the population structure of 27 high-alpine plants

A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem and historical factors. As a result, many different statistical methods exist that measure different aspects of species' genetic structure. However, little is known about how these methods are interrelated and how they are related to a species' ecology and life history. In this study, we used the IntraBioDiv amplified fragment length polymorphisms data set from 27 high-alpine species to calculate eight genetic summary statistics that we jointly correlate to a set of six ecological and life-history traits. We found that there is a large amount of redundancy among the calculated summary statistics and that there is a significant association with the matrix of species traits. In a multivariate analysis, two main aspects of population structure were visible among the 27 species. The first aspect is related to the species' dispersal capacities and the second is most likely related to the species' postglacial recolonization of the Alps. Furthermore, we found that some summary statistics, most importantly Mantel's r and Jost's D, show different behaviour than expected based on theory. We therefore advise caution in drawing too strong conclusions from these statistics.