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As a result of the scarcity of informative morphological and anatomical characters, nematode systematics have always been volatile. Differences in the appreciation of these characters have resulted in numerous classifications and this greatly confuses scientific communication. An advantage of the use of molecular data is that it allows for an enormous expansion of the number of characters. Here we present a phylogenetic tree based on 1215 small subunit ribosomal DNA sequences (ca 1700 bp each) covering a wide range of nematode taxa. Of the 19 nematode orders mentioned by De Ley et al. (2006) 15 are represented here. Compared with Holterman et al. (2006) the number of taxa analysed has been tripled. This did not result in major changes in the clade subdivision of the phylum, although a decrease in the number of well supported nodes was observed. Especially at the family level and below we observed a considerable congruence between morphology and ribosomal DNA-based nematode systematics and, in case of discrepancies, morphological or anatomical support could be found for the alternative grouping in most instances. The extensiveness of convergent evolution is one of the most striking phenomena observed in the phylogenetic tree presented here - it is hard to find a morphological, ecological or biological characteristic that has not arisen at least twice during nematode evolution. Convergent evolution appears to be an important additional explanation for the seemingly persistent volatility of nematode systematics. [ABSTRACT FROM AUTHOR]

In the detection of plant pests, speed and accuracy are vital. High-resolution melting curve (HRMC) analysis was therefore evaluated as a new tool for the identification of root-knot nematodes ( Meloidogyne spp.). On the basis of the second intergenic spacer (IGS2) region of the ribosomal DNA cistron, Meloidogyne chitwoodi, M. fallax and M. hapla were successfully distinguished from each other and the group of the three tropical species, M. incognita, M. arenaria and M. javanica. Conversely, it was shown that the IGS2 region is not suitable for the tropical species M. enterolobii (senior synonym of M. mayaguensis) as the amplification of multiple fragments of different lengths prevented a reliable HRMC analysis. However, the obtained results provide a proof of principle that HRMC analysis can be a suitable single-tube assay for fast and accurate root-knot nematode identification. [ABSTRACT FROM AUTHOR]

Biological indicators are highly relevant for assessing the condition of a soil as they are integrative; they reflect the overall impact of physical, chemical and biological changes. Indigenous soil organisms are preferable to other test organisms because the diversity and condition of indigenous soil organisms reflect both acute and chronic effects of soil disturbances. Nematodes are ubiquitous, speciose, easily extractable and present in extremely high numbers. Given the ever increasing amount of sequence data, DNA barcode-based community analysis will soon be possible and a next step would be to define objective criteria for the ecological grouping of soil nematodes. Here, we present a framework to ascertain which traits are correlated with a tolerance to stress. For this, a field study on the effects of pH and copper on nematode communities was re-analysed. Changes in abundances of individual genera were correlated with a number of potentially stress tolerance-related characteristics. The generalised least squares (GLS) method was used to account for the phylogenetic dependence of the data. Only the relationship between the ability to enter a survival stage and tolerance to copper at pH 6.1 was found to be significant, but the quantity of missing data probably had a negative impact on the analyses. This study did, however, clearly demonstrate the importance of accounting for the effects of phylogenetic dependence in the data. When the phylogeny was taken into account, we observed an average change in P value of 0.196 (and in some cases as much as 0.6) for the correlations of possible stress-related characteristics and Cu or pH tolerance. This research constitutes a proof-of-principle for a transparent method to relate stress tolerance to (ecological) characteristics. The usefulness of this powerful method should become even clearer when substantially higher numbers of individuals are analysed (as facilitated by using DNA barcodes) and when missing data are filled in. [ABSTRACT FROM AUTHOR]

Potato cyst nematodes (PCNs), the umbrella term for Globodera rostochiensis and G. pallida, coevolved with their Solanaceous hosts in the Andean Mountain region. From there, PCN proliferated worldwide to virtually all potato production areas. PCN is a major factor limiting the potato production in Indonesia. In our survey, only G. rostochiensis was found. Fourteen field populations were collected on Java and Sumatra, and unique variants were called by mapping resequencing data on a G. rostochiensis reference genome. A phylogenetic tree based on 1.4 million unique variants showed a genotypic separation between the outgroup, a Scottish Ro1 population, and all Indonesian populations. This separation was comparable in size with the genotypic distinction between the Javanese and the Sumatran PCN populations. Next, variants within PCN effector gene families SPRYSEC, 1106, 4D06, and venom allergen-like protein (VAL) that all interfere with the host innate immune system were compared. Distinct selective pressures acted on these effector families; while SPRYSECs (4,341 single-nucleotide polymorphisms [SNPs]/insertions or deletions of bases [indels]) behaved like neutral genes, the phylogenetic trees of 1106, 4D06, and VAL proteins (235, 790, and 150 SNPs/indels, respectively) showed deviating topologies. Our data suggest that PCN was introduced on Java not too long after the introduction of potato in the middle of the eighteenth century. Soon thereafter, the pathogen established on Sumatra and started to diversify independently. This scenario was corroborated by diversification patterns of the effector families 1106, 4D06, and VAL. Our data demonstrate how genome resequencing data from a nonindigenous pathogen can be used to reconstruct the introduction and diversification process. [ABSTRACT FROM AUTHOR]

Potato cyst nematodes (PCNs), the umbrella term for Globodera rostochiensis and G. pallida , coevolved with their Solanaceous hosts in the Andean Mountain region. From there, PCN proliferated worldwide to virtually all potato production areas. PCN is a major factor limiting the potato production in Indonesia. In our survey, only G . rostochiensis was found. Fourteen field populations were collected on Java and Sumatra, and unique variants were called by mapping resequencing data on a G . rostochiensis reference genome. A phylogenetic tree based on 1.4 million unique variants showed a genotypic separation between the outgroup, a Scottish Ro1 population, and all Indonesian populations. This separation was comparable in size with the genotypic distinction between the Javanese and the Sumatran PCN populations. Next, variants within PCN effector gene families SPRYSEC, 1106, 4D06, and venom allergen-like protein (VAL) that all interfere with the host innate immune system were compared. Distinct selective pressures acted on these effector families; while SPRYSECs (4,341 single-nucleotide polymorphisms [SNPs]/insertions or deletions of bases [indels]) behaved like neutral genes, the phylogenetic trees of 1106, 4D06, and VAL proteins (235, 790, and 150 SNPs/indels, respectively) showed deviating topologies. Our data suggest that PCN was introduced on Java not too long after the introduction of potato in the middle of the eighteenth century. Soon thereafter, the pathogen established on Sumatra and started to diversify independently. This scenario was corroborated by diversification patterns of the effector families 1106, 4D06, and VAL. Our data demonstrate how genome resequencing data from a nonindigenous pathogen can be used to reconstruct the introduction and diversification process.