Molecular evidence that the genes for dioecism and monoecism in Spinacia oleracea L. are located at different loci in a chromosomal region

Spinach (Spinacia oleracea L.) is widely known to be dioecious. However, monoecious plants can also occur in this species. Sex expression in dioecious spinach plants is controlled by a single gene pair termed X and Y. Our previous study showed that a single, incompletely dominant gene, which controls the monoecious condition in spinach line 03–336, should be allelic or linked to X/Y. Here, we developed 19 AFLP markers closely linked to the monoecious gene. The AFLP markers were mapped to a 38.2-cM chromosomal region that included the monoecious gene, which is bracketed between flanking markers with a distance of 7.1 cM. The four AFLP markers developed in our studies were converted into sequence-characterized amplified region (SCAR) markers, which are linked to both the monoecious gene and Y and are common to both populations segregating for the genes. Linkage analysis using the SCAR markers suggested that the monoecious gene (M) and Y are located in different intervals, between different marker pairs. Analysis of populations segregating for both M and Y also directly demonstrates linkage of the genes at a distance of ∼12 cM. The data presented in this study may be useful for breeding dioecious and highly male monoecious lines utilized as the pollen parents for hybrid seed production, as well as for studies of the evolutionary history of sexual systems in this species, and can provide a molecular basis for positional cloning of the sex-determining genes.     

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.     

Larval identification of Lutjanus Bloch in Nansha coral reefs by AFLP molecular method

Species of Lutjanus Bloch are highly valued fish in some fisheries of the world and some species are cultured in the Southeast Asia especially in South China. Wild larvae are still the major source of mariculture in South China because artificial breeding techniques for most Lutjanus species have not yet been available. The Nansha coral reefs (also called Spratly Archipelago) water area, which is located in the South China Sea, is the main habitat and spawn area for Lutjanus in China. Larval identification of Lutjanus is important for relative ecological studies and mariculture, but larvae of many closely related species, such as those of the genus Lutjanus, are different to be distinguished morphologically. In the present study, a PCR-based fingerprinting technique called amplified fragment length polymorphism AFLP was used in the characterization and identification of 11 Lutjanus species captured in Nansha coral reefs. Optimal AFLP patterns were obtained with primer combination of E+AGC/M+CAA selective nucleotides. There were in total 132 AFLP loci in all specimens, and AFLP markers of each species varied from 44 to 69, but only 7 markers were fixed in all specimens. Meanwhile, high levels of intraspecific homogeneity were observed. All 11 species of Lutjanus were successfully identified by the comparative analyses of AFLP patterns. Moreover, neighbour-joining and UPGMA analyses of AFLP data were compared with current morphological taxonomic systems.     

AFLP assessment of genetic diversity among Indian Mucuna accessions

Amplified fragment length polymorphism (AFLP) marker was used to assess diversity in germplasm collection of Mucuna species which has gained tremendous attention in the recent past due to its promising nutritional, agronomic and medicinal attributes. Twenty five accessions comprising five species, collected from seven states of India were evaluated with twelve AFLP primer combinations that generated a total of 1,612 fragments with an average of 134 fragments per primer combination. The values of polymorphic information content (PIC), marker index (MI) and the resolving power (Rp) demonstrated the utility of the primer combinations used in the present study for discriminating the Mucuna accessions. UPGMA and Principal coordinate analysis (PCoA) of the genotypic data revealed clustering of accessions as per phenetic and genetic relationships. The Jaccard’s similarity coefficient values suggested good variability among the M. pruriens accessions indicating their utility in breeding programs. Molecular diversity presented in this study combined with the datasets on other morphological/agronomic traits will be highly useful for selecting appropriate accessions for plant improvement through conventional as well as molecular breeding approaches and for evolving suitable conservation strategies.     

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.     

Genetic comparison of Bacillus anthracis and its close relatives using amplified fragment length polymorphism and polymerase chain reaction analysis

Amplified fragment length polymorphism (AFLP) analysis allows a rapid, relatively simple analysis of a large portion of a microbial genome, providing information about the species and its phylogenetic relationship to other microbes (Vos et al. 1995). The method simply surveys the genome for length and sequence polymorphisms. The AFLP pattern identified can be used for comparison to the genomes of other species. Unlike other methods, it does not rely on analysis of a single genetic locus that may bias the interpretation of results and does not require any prior knowledge of the targeted organism. Moreover, a standard set of reagents can be applied to any species without using species-specific information or molecular probes. We are using AFLP analysis to rapidly identify different bacterial species. A comparison of AFLP profiles generated from a large battery of Bacillus anthracis strains shows very little variability among different isolates (Keim et al. 1997). By contrast, there is a significant difference between AFLP profiles generated for any B. anthracis strain and even the most closely related Bacillus species. Sufficient variability is apparent among all known microbial species to allow phylogenetic analysis based on large numbers of genetically unlinked loci. These striking differences among AFLP profiles allow unambiguous identification of previously identified species and phylogenetic placement of newly characterized isolates relative to known species based on a large number of independent genetic loci. Data generated thus far show that the method provides phylogenetic analyses that are consistent with other widely accepted phylogenetic methods. However, AFLP analysis provides a more detailed analysis of the targets and samples a much larger portion of the genome. Consequently, it provides an inexpensive, rapid means of characterizing microbial isolates to further differentiate among strains and closely related microbial species. Such information cannot be rapidly generated by other means. AFLP sample analysis quickly generates a very large amount of molecular information about microbial genomes. However, this information cannot be analysed rapidly using manual methods. We are developing a large archive of electronic AFLP signatures that is being used to identify isolates collected from medical, veterinary, forensic and environmental samples. We are also developing the computational packages necessary to rapidly and unambiguously analyse the AFLP profiles and conduct a phylogenetic comparison of these data relative to information already in our database. We will use this archive and the associated algorithms to determine the species identity of previously uncharacterized isolates and place them phylogenetically relative to other microbes based on their AFLP signatures. This study provides significant new information about microbes with environmental, veterinary and medical significance. This information can be used in further studies to understand the relationships among these species and the factors that distinguish them from one another. It should also allow the identification of unique factors that contribute to important microbial traits, including pathogenicity and virulence. We are also using AFLP data to identify, isolate and sequence DNA fragments that are unique to particular microbial species and strains. The fragment patterns and sequence information provide insights into the complexity and organization of bacterial genomes relative to one another. They also provide the information necessary for the development of species-specific polymerase chain reaction primers that can be used to interrogate complex samples for the presence of B. anthracis, other microbial pathogens or their remnants.     

Genetic divergence of Trichogramma aurosum Sugonjaev and Sorokina (Hymenoptera: Trichogrammatidae) individuals based on ITS2 and AFLP analysis

Taxonomy and phylogeny of members of the genus Trichogramma is often critical because of the fact that proper species discrimination can only be achieved by male morphology. Cryptic species, particularly when only females are available (in case of parthenogenetic species or strains), are common in this genus with consequences for practical purposes like biocontrol, unless males can be obtained after antibiotic treatment. The internally transcribed spacer 2 region of the ribosomal DNA was used to assess the identity of Trichogramma aurosum Sugonjaev and Sorokina individuals collected on eggs of Nematus tibialis Newman (Hymenoptera: Tenthredinidae) from different locations in Middle Europe. Amplified products were identical in length (ca. 450bp), sequences showed a high percent similarity (>96%), and no cryptic species could be detected in the samples. In contrast, a comparison with T. aurosum populations from the USA showed values between 86% and 90%. Additional studies are needed to clarify the relationship between US and European populations. Furthermore, amplified fragment length polymorphism (AFLP) analysis was conducted with T. aurosum wasps collected at 25 different European locations. One hundred and twenty‐three AFLP fragments could be detected using three different AFLP primer combinations of which 98% were polymorphic in more than one individual. An analysis of genetic distances based on the obtained AFLP markers indicated the existence of some genetic variability between the European T. aurosum individuals and allowed a grouping according to their geographic origin. This study represents the first successful application of the AFLP marker technique to such tiny insects as Trichogramma species.     

The status of AFLP in the genomics era and a pipeline for converting AFLPs into single-locus markers

Even though next-generation sequencing (NGS) has now become the predominant state-of-the-art technique for genotyping populations, amplified fragment length polymorphism (AFLP) DNA fingerprinting is still a relevant method, thanks to its versatility, cost-effectiveness, independence of prior sequence information and broad applicability. Even though the number of AFLP studies reached its peak in 2012, it is still applied extensively for phylogenetic analysis, genotyping or identifying non-model species, which often feature complex and large genomes. For these purposes, tools continue to be developed for designing AFLP studies, scoring AFLPs or handling AFLP data. Moreover, AFLP studies embrace the NGS technology; for example, the whole-genome sequence of model species is used to design more efficient AFLP studies for non-model species. Conversely, in complexity reduction of polymorphic sequences and restriction site-associated DNA sequencing studies, polymorphisms are often found to be present in many restriction sites, which can still be studied as AFLPs. We discuss the latest advances in AFLP-based studies in the era of NGS and anticipate that AFLP will remain a relevant method in the near future, even for species with a known genome, owing to its many promising new features such as methylation-sensitive-AFLP. Here, we also present an optimized pipeline for converting AFLP markers into single-locus markers, which can be applied in both traditional AFLP and NGS studies.     

Use of AFLP and RAPD molecular genetic markers and cytogenetic analysis to explore relationships among taxa of the Patagonian Bromus setifolius complex

Bromus setifolius var. pictus (Hook) Skottsb., B. setifolius var. setifolius Presl. and B.setifolius var. brevifolius Ness are three native Patagonian taxa in the section Pnigma Dumort of the genus Bromus L. AFLP and RAPD analysis, in conjunction with genetic distance measurements and statistical techniques, revealed variation within this group and indicated that B. setifolius var. brevifolius was closely related to B. setifolius var. pictus, with both taxa being more distantly related to B. setifolius var. setifolius. Cytogenetic analysis confirmed the chromosomal number of B. setifolius var. pictus (2n = 70) and B. setifolius var. setifolius (2n = 28) and showed for the first time that B. setifolius var. brevifolius had 2n = 70. The combination of molecular genetic and cytogenetic evidence supported a species status for two of the three taxa and suggested hypotheses for the evolutionary origin of these complex taxa. Species status was also indicated for B. setifolius var. setifolius. Based on these findings, we suggest that B. setifolius var. pictus be referred to as B. pictus Hook var. pictus, and B. setifolius var brevifolius as B. pictus Hook var brevifolius. The correlation between AFLP diversity and variation in ecological parameters suggested that this marker system could be used to assess breeding progress and to monitor the domestication of Patagonian Bromus species for agronomic use.     

Molecular evidence for hybridization in Colias (Lepidoptera: Pieridae): are Colias hybrids really hybrids?

Gene flow and hybridization among species dramatically affect our understanding of the species as a biological unit, species relationships, and species adaptations. In North American Colias eurytheme and Colias eriphyle, there has been historical debate over the extent of hybridization occurring and the identity of phenotypically intermediate individuals as genetic hybrids. This study assesses the population structure of these two species to measure the extent of hybridization and the genetic identity of phenotypic intermediates as hybrids. Amplified fragment length polymorphism (AFLP) marker analysis was performed on 378 specimens collected from northern California and Nevada. Population structure was inferred using a Bayesian/Markov chain Monte Carlo method, which probabilistically assigns individuals to genetic clusters. Three genetic clusters provided the best fit for the data. C. eurytheme individuals were primarily assigned to two closely related clusters, and C. eriphyle individuals were mostly assigned to a third, more distantly related cluster. There appeared to be significant hybridization between the two species. Individuals of intermediate phenotype (putative hybrids) were found to be genetically indistinguishable from C. eriphyle, indicating that previous work based on the assumption that these intermediate forms are hybrids may warrant reconsideration.     

Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp,Cyprinus carpio L.

Genetic relationships among eight populations of domesticated carp (Cyprinus carpio L.), a species with a partially duplicated genome, were studied using 12 microsatellites and 505 AFLP bands. The populations included three aquacultured carp strains and five ornamental carp (koi) variants. Grass carp (Ctenopharyngodon idella) was used as an outgroup. AFLP-based gene diversity varied from 5% (grass carp) to 32% (koi) and reflected the reasonably well understood histories and breeding practices of the populations. A large fraction of the molecular variance was due to differences between aquacultured and ornamental carps. Further analyses based on microsatellite data, including cluster analysis and neighbor-joining trees, supported the genetic distinctiveness of aquacultured and ornamental carps, despite the recent divergence of the two groups. In contrast to what was observed for AFLP-based diversity, the frequency of heterozygotes based on microsatellites was comparable among all populations. This discrepancy can potentially be explained by duplication of some loci in Cyprinus carpio L., and a model that shows how duplication can increase heterozygosity estimates for microsatellites but not for AFLP loci is discussed. Our analyses in carp can help in understanding the consequences of genotyping duplicated loci and in interpreting discrepancies between dominant and co-dominant markers in species with recent genome duplication.     

AFLP analysis of genetic relationships among papaya and its wild relatives (Caricaceae) from Ecuador

The AFLP technique was used to assess the genetic relationships among the cultivated papaya ( Carica papaya L.) and related species native to Ecuador. Genetic distances based on AFLP data were estimated for 95 accessions belonging to three genera including C. papaya, at least eight Vasconcella species and two Jacaratia species. Cluster analysis using different methods and principal co-ordinate analysis (PCO), based on the AFLP data from 496 polymorphic bands generated with five primer combinations, was performed. The resulted grouping of accessions of each species corresponds largely with their taxonomic classifications and were found to be consistent with other studies based on RAPD, isozyme and cpDNA data. The AFLP analysis supports the recent rehabilitation of the Vasconcella group as a genus; until recently Vasconcella was considered as a section within the genus Carica. Both cluster and PCO analysis clearly separated the species of the three genera and illustrated the large genetic distance between C. papaya accessions and the Vasconcella group. The specific clustering of the highly diverse group of Vasconcella x heilbornii accessions also suggests that these genotypes may be the result of bi-directional introgression events between Vasconcella stipulata and Vasconcella cundinamarcensis.     

Convergence in pigmentation at multiple levels: mutations,genes and function

Convergence—the independent evolution of the same trait by two or more taxa—has long been of interest to evolutionary biologists, but only recently has the molecular basis of phenotypic convergence been identified. Here, we highlight studies of rapid evolution of cryptic coloration in vertebrates to demonstrate that phenotypic convergence can occur at multiple levels: mutations, genes and gene function. We first show that different genes can be responsible for convergent phenotypes even among closely related populations, for example, in the pale beach mice inhabiting Florida''s Gulf and Atlantic coasts. By contrast, the exact same mutation can create similar phenotypes in distantly related species such as mice and mammoths. Next, we show that different mutations in the same gene need not be functionally equivalent to produce similar phenotypes. For example, separate mutations produce divergent protein function but convergent pale coloration in two lizard species. Similarly, mutations that alter the expression of a gene in different ways can, nevertheless, result in similar phenotypes, as demonstrated by sister species of deer mice. Together these studies underscore the importance of identifying not only the genes, but also the precise mutations and their effects on protein function, that contribute to adaptation and highlight how convergence can occur at different genetic levels.     

Pattern and timing of diversification in Yucca (Agavaceae): specialized pollination does not escalate rates of diversification

The yucca-yucca moth interaction is one of the most well-known and remarkable obligate pollination mutualisms, and is an important study system for understanding coevolution. Previous research suggests that specialist pollinators can promote rapid diversification in plants, and theoretical work has predicted that obligate pollination mutualism promotes cospeciation between plants and their pollinators, resulting in contemporaneous, parallel diversification. However, a lack of information about the age of Yucca has impeded efforts to test these hypotheses. We used analyses of 4322 AFLP markers and cpDNA sequence data representing six non-protein-coding regions (trnT-trnL, trnL, trnL intron, trnL-trnF, rps16 and clpP intron 2) from all 34 species to recover a consensus organismal phylogeny, and used penalized likelihood to estimate divergence times and speciation rates in Yucca. The results indicate that the pollination mutualism did not accelerate diversification, as Yucca diversity (34 species) is not significantly greater than that of its non-moth-pollinated sister group, Agave sensu latissimus (240 species). The new phylogenetic estimates also corroborate the suggestion that the plant-moth pollination mutualism has at least two origins within the Agavaceae. Finally, age estimates show significant discord between the age of Yucca (ca 6-10Myr) and the current best estimates for the age of their pollinators (32-40Myr).     

Challenges and pitfalls in the characterization of anonymous outlier AFLP markers in non-model species: lessons from an ocellated lizard genome scan

In the last few years, dozens of studies have documented the detection of loci influenced by selection from genome scans in a wide range of non-model species. Many of those studies used amplified fragment length polymorphism (AFLP) markers, which became popular for being easily applicable to any organism. However, because they are anonymous markers, AFLPs impose many challenges for their isolation and identification. Most recent AFLP genome scans used capillary electrophoresis (CE), which adds even more obstacles to the isolation of bands with a specific size for sequencing. These caveats might explain the extremely low number of studies that moved from the detection of outlier AFLP markers to their actual isolation and characterization. We document our efforts to characterize a set of outlier AFLP markers from a previous genome scan with CE in ocellated lizards (Lacerta lepida). Seven outliers were successfully isolated, cloned and sequenced. Their sequences are noncoding and show internal indels or polymorphic repetitive elements (microsatellites). Three outliers were converted into codominant markers by using specific internal primers to sequence and screen population variability from undigested DNA. Amplification in closely related lizard species was also achieved, revealing remarkable interspecific conservation in outlier loci sequences. We stress the importance of following up AFLP genome scans to validate selection signatures of outlier loci, but also report the main challenges and pitfalls that may be faced during the process.     

Metabolomics of forage plants: a review

Background

Forage plant breeding is under increasing pressure to deliver new cultivars with improved yield, quality and persistence to the pastoral industry. New innovations in DNA sequencing technologies mean that quantitative trait loci analysis and marker-assisted selection approaches are becoming faster and cheaper, and are increasingly used in the breeding process with the aim to speed it up and improve its precision. High-throughput phenotyping is currently a major bottle neck and emerging technologies such as metabolomics are being developed to bridge the gap between genotype and phenotype; metabolomics studies on forages are reviewed in this article.

Scope

Major challenges for pasture production arise from the reduced availability of resources, mainly water, nitrogen and phosphorus, and metabolomics studies on metabolic responses to these abiotic stresses in Lolium perenne and Lotus species will be discussed here. Many forage plants can be associated with symbiotic microorganisms such as legumes with nitrogen fixing rhizobia, grasses and legumes with phosphorus-solubilizing arbuscular mycorrhizal fungi, and cool temperate grasses with fungal anti-herbivorous alkaloid-producing Neotyphodium endophytes and metabolomics studies have shown that these associations can significantly affect the metabolic composition of forage plants. The combination of genetics and metabolomics, also known as genetical metabolomics can be a powerful tool to identify genetic regions related to specific metabolites or metabolic profiles, but this approach has not been widely adopted for forages yet, and we argue here that more studies are needed to improve our chances of success in forage breeding.

Conclusions

Metabolomics combined with other ‘-omics’ technologies and genome sequencing can be invaluable tools for large-scale geno- and phenotyping of breeding populations, although the implementation of these approaches in forage breeding programmes still lags behind. The majority of studies using metabolomics approaches have been performed with model species or cereals and findings from these studies are not easily translated to forage species. To be most effective these approaches should be accompanied by whole-plant physiology and proof of concept (modelling) studies. Wider considerations of possible consequences of novel traits on the fitness of new cultivars and symbiotic associations need also to be taken into account.     

Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters

Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified fragment length polymorphisms (AFLPs) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff between culling all but the lowest-error loci to minimize overall genotyping error versus the potential for increasing population genetic signal by retaining more loci. Here, we used AFLPs to compare population structure in co-distributed broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris) oyster species. Using existing methods for almost entirely automated marker selection and scoring, genotyping error tradeoffs were evaluated by comparing results across a nested series of data sets with mean mismatch errors of 0, 1, 2, 3, 4 and >4%. Artifactual population structure was diagnosed in high-error data sets and we assessed the low-error point at which expected population substructure signal was lost. In both species, we identified substructure patterns deemed to be inaccurate at average mismatch error rates 2 and >4%. In the species comparison, the optimum data sets showed higher gene flow for the brooding oyster with more oceanic salinity tolerances. AFLP tradeoffs may differ among studies, but our results suggest that important signal may be lost in the pursuit of 'acceptable' error levels and our procedures provide a general method for empirically exploring these tradeoffs.     

Genome wide AFLP markers support cryptic species in Coniophora (Boletales)

Numerous fungal morphospecies include cryptic species that routinely are detected by sequencing a few unlinked DNA loci. However, whether the patterns observed by multi-locus sequencing are compatible with genome wide data, such as amplified fragment length polymorphisms (AFLPs), is not well known for fungi. In this study we compared the ability of three DNA loci and AFLP data to discern between cryptic fungal lineages in the three morphospecies Coniophora olivacea, Coniophora arida, and Coniophora puteana. The sequences and the AFLP data were highly congruent in delimiting the morphotaxa into multiple cryptic species. However, while the DNA sequences indicated introgression or hybridization between some of the cryptic lineages the AFLP data did not. We conclude that as few as three polymorphic DNA loci was sufficient to recognize cryptic lineages within the studied Coniophora taxa. However, based on analyses of a few (three) sequenced loci the hybridization could not easily be distinguished from incomplete lineage sorting. Hence, great caution should be taken when concluding about hybridization based on data from just a few loci.     

Molecular genetic evidence for parthenogenesis in the Burmese python,Python molurus bivittatus

Parthenogenesis among reptiles is rare. Only a few species have the ability to reproduce asexually. Most of these are obligate parthenogenetic species that consist (almost) entirely of females, which can reproduce solely through parthenogenesis. Rarer are sexual species that only sporadically reproduce through parthenogenesis. A female Python molurus bivittatus (Reptilia, Boidae) from the Artis Zoo, Amsterdam, produced eggs in five consecutive years that contained embryos while she was isolated from males. These eggs might be fertilized with stored sperm, or might be the product of parthenogenesis. Parthenogenesis has not been shown for the Boidae family before. We performed parentship analyses on the snake and seven of her embryos using microsatellites and AFLP. Four microsatellite loci developed for this species combined with three loci developed previously for different snake species revealed too little variation to discriminate between sperm retention and parthenogenesis. With AFLP we were able to confirm that the Artis Zoo female reproduced parthenogenetically. Because the offspring are genetically identical to their mother, whereas in previous studies on sporadic parthenogenesis in snakes a loss of genetic information was reported, we conclude that the meiotic pathways that produce the diploid egg cells are different.     

Global patterns reveal strong population structure in Haemonchus contortus, a nematode parasite of domesticated ruminants

We have examined the global population genetic structure of Haemonchus contortus. The genetic variability was studied using both amplified fragment length polymorphism (AFLP) and nad4 sequences of the mitochondrial genome. To examine the performance and information content of the two different marker systems, comparative assessment of population genetic diversity was undertaken in 19 isolates of H. contortus, a parasitic nematode of small ruminants. A total of 150 individual adult worms representing 14 countries from all inhabited continents were analysed. Altogether 1,429 informative AFLP markers were generated using four different primer combinations. Also, the genetic variation was high, which agrees with results from previous AFLP studies of nematode parasites of livestock. The genetic structure was high, indicating limited gene flow between the different isolates and populations from each continent mostly formed monophyletic groups in the phylogenetic analysis. However, for isolates representing Australia, Greece and one laboratory strain that originated from South Africa (WRS), there was no clear genetic relationship between the isolates and the distance between their geographical origins. Basically the same pattern was observed for the mitochondrial marker, although the phylogenetic analysis was less resolved than for AFLP. In contrast with previous findings on the population genetic structure of H. contortus, the calculation of population structure gave high values (Nst=0.59). The strong structure was present also for the four Swedish isolates (Nst=0.16) representing a small geographical area.