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A northward colonisation of the Andes by the potato cyst nematode during geological times suggests multiple host shifts from wild to cultivated potatoes
Abstract
The cyst nematode Globodera pallida is a major pest of potato in South America where this specialist parasite is native. To investigate its phylogeography, we have genotyped individuals from 42 Peruvian populations using mitochondrial and nuclear molecular markers. A clear south-to-north phylogeographical pattern was revealed with five well-supported clades. The clade containing the southern populations is genetically more diverse and forms the most basal branch. The large divergence among cytochrome b haplotypes suggests that they diverged before human domestication of potato. As the nematodes studied have been sampled on cultivated potato, multiple host-shifts from wild to cultivated potatoes must have occurred independently in each clade. We hypothesise that this south-to-north pattern took place during the uplift of the Andes beginning 20 My ago and following the same direction. To our knowledge, this is the first study of a plant parasite sampled on cultivated plants revealing an ancient phylogeographical pattern.
Supplementary resources (33)
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... The cytochrome b gene of mitochondrial DNA (mtDNA) has been used for relationship analysis among geographic populations of G. pallida (Madani et al. 2010;Ohki et al. 2018;Picard et al. 2007;Plantard et al. 2008). The set of primers, INRAcytbL and INRAcytbR, developed by Picard et al. (2007) to amplify the cytochrome b gene of G. pallida differs by several nucleotides from the corresponding sequence of G. rostochiensis. ...
... The cytochrome b gene of mitochondrial DNA (mtDNA) has been used for relationship analysis among geographic populations of G. pallida (Madani et al. 2010;Ohki et al. 2018;Picard et al. 2007;Plantard et al. 2008). The set of primers, INRAcytbL and INRAcytbR, developed by Picard et al. (2007) to amplify the cytochrome b gene of G. pallida differs by several nucleotides from the corresponding sequence of G. rostochiensis. These primers were expected to specifically detect G. pallida. ...
... The amplicon size of this primer set was 530 bp. The primers INRAcytbL and INRAcytbR (Picard et al. 2007), which were initially considered as G. pallida-specific primers, did not amplify the DNA when a large number of G. rostochiensis nematodes and a very small population of G. pallida coexisted, as prepared in model G. While the simplex PCR using this primer set alone detected G. pallida, this species was not detected in the duplex PCR when that primer set was used with the primer set for G. rostochiensis in the same reaction conditions. ...
A simple, inexpensive technique has been needed to detect and distinguish the potato cyst nematodes Globodera rostochiensis and G. pallida, major pests of potatoes. We thus developed a sensitive duplex polymerase chain reaction (PCR) method using primers for the mitochondrial DNA’s cytochrome b gene region and agarose gel electrophoresis to identify G. rostochiensis and G. pallida and an efficient method to extract nematode DNA by crushing cysts in the presence of soil impurities. These methods provided the sensitivity to detect one egg of the target species, even if the extracted DNA solution was contaminated with PCR inhibitors derived from impurities. In addition, when the two species are both present in a sample at greatly different numbers, this method aided in detecting and identifying them accurately. The method will greatly benefit inspection institutions and advance the design of strategies to control these nematodes.
... Il sera alors montré que les populations péruviennes possèdent une diversité génétique supérieure à celle observée pour les populations européennes (Bendezu et al., 1998). Suite à un échantillonnage conséquent effectué au Pérou, la structure des populations de G. pallida ainsi que l'aire d'origine de l'espèce G. pallida, où la diversité Picard et al. (2007Picard et al. ( , 2008. Répartition des différents clades génétiques observés chez G. pallida au Pérou et relations phylogénétiques. ...
... génétique est la plus élevée, ont pu être identifiées. Clairement, le sud du Pérou est la zone de diversité maximale des populations de G. pallida, c'est également à partir de cette zone que semblent avoir été importées toutes les populations européennes connues à ce jour (Picard et al., 2007. (Grenier et al., 2010 ;Subbotin et al., 2010 ;Lax et al., 2013). ...
... (Grenier et al., 2010 ;Subbotin et al., 2010 ;Lax et al., 2013). Les taux de divergence nucléotidique mesurées pour le marqueur cytb entre les cinq clades atteignent près de 12% (Picard et al., 2007) soit autant que la divergence rapportée entre les espèces C. elegans et C. briggsae (Stein et al., 2003). Les analyses génétiques basées sur un séquençage ITS-rDNA, incluant des représentants de ces clades ainsi que d'autres populations de G. pallida, notamment des populations chiliennes, démontreront la diversité contenue à l'intérieur de l'espèce (Subbotin et al., 2011). ...
Les nématodes à kyste du genre Globodera sont parmi les phytoparasites les plus étudiés de par l’impact économique qu’ils peuvent engendrer sur les productions agricoles. Originaire des hauts plateaux de la cordillère des Andes ce genre aurait été importé en Europe à la fin du XIX siècle. L’existence d’un complexe d’espèce cryptique chez G. pallida, nématode phytoparasites d’importance au sein du genre, est questionnée. La révision taxonomique de cette espèce peut avoir des conséquences fortes en termes d’épidémiologie, d’évaluation et de gestion des risques. Durant ce travail une approche de taxonomie intégrative impliquant trois champs disciplinaires, génétique, morphométrique et biologique, a été développée sur un panel de populations sud-américaines pour délimiter de nouvelles frontières au sein de cette espèce. L’exploration de la diversité génétique a permis de révéler l’exitence de deux groupes fortement distants de G. pallidaCette étude questionne aussi les processus impliqués dans cette divergence qui semblent distincts pour ces deux groupes. L’existence d’une différenciation morphologique a été observée grâce à un outil d’analyse d’image automatisé créé spécifiquement pour ce travail. Le développement de l’outil constitue une approche novatrice pour l’étude de la morphométrie dans ce genre et plus généralement chez les nématodes. Cette différenciation s’appuie sur l’intégration combinée de trois métriques adaptées à la morphométrie automatisée. Enfin, l’étude de la capacité de ces entités à se développer aux dépens de certaines plantes a elle aussi rapporté des
... Our case study involved the cyst nematode Globodera pallida, one of the major pest of potato crop worldwide (Oerke et al., 2012, Turner & Evans, 1998 This nematode originated from the Andean region of South-America, the origin of its wild host potatoes and other Solanum species (Evans & Stone, 1977, Hijmans & Spooner, 2001. Its main range lies in Peru where Picard et al. (2007) highlighted five distinct genetic clades with a southto-north pattern associated to a decreasing genetic diversity. G. pallida is a sedentary endoparasite. ...
... Moreover, regarding the nematode population effect, there was no impact of G. pallida genetic clades (Picard et al., 2007) on the hatching of juveniles. This result could be due to a differential adaptation of each G. pallida population to contrasted local climate conditions (i.e. ...
... Brassicaceae, Polygonaceae or also Solanaceae families (Turner & Subbotin, 2013), Globodera pallida, the potato cyst nematode, attacks the potato and others species of Solanum such as tomato and eggplant (Sullivan et al., 2007) and Heterodera carotae, the carrot cyst nematode, is highly specific and its development is restricted to the genera Daucus and Torilis (Aubert, 1986). Instead of choosing the different populations randomly, we made a choice based on the known spatial genetic structure of the three nematode species (Picard et al., 2007, Plantard et al., 2008. Those genetic structures being based on neutral markers (microsatellites), we used here the fact that, for species with a low dispersal capability, such as nematodes, the neutral evolutionary history could be highly correlated to phenotypic specificities. ...
Les nématodes à kyste sont d’importants parasites des cultures, causant des pertes économiques élevées. Chez ces nématodes, l'éclosion est stimulée par les exsudats radiculaires libérés par la plante hôte. Le retrait des derniers nématicides nécessite le développement de solutions alternatives pour protéger les cultures. Ainsi, l’utilisation d’exsudats radiculaires pour provoquer une « éclosion suicide » des nématodes en l’absence de plantes hôtes représente un intérêt dans le management de ces parasites. Cette thèse visait à anticiper l'efficacité de cette stratégie, en prenant compte la diversité génétique côté nématodes et la composition microbiotique des sols. Tout d’abord, le niveau de dépendance entre les exsudats radiculaires d'espèces sauvages de Solanum et les populations de Globodera pallida sur le trait de vie éclosion a étéévalué et a mis en évidence un effet fort de la provenance géographique des exsudats. Ensuite les exsudats radiculaires de différentes espèces végétales ont été testés sur l'éclosion de populations représentatives de la diversité génétique de trois nématodes à kyste. Malgré des différences significatives obtenues entre les populations pour une espèce de nématode donnée, les exsudats radiculaires permettent une éclosion importante des nématodes. Enfin, l'impact des communautés microbiennes du sol sur l'efficacité des exsudats radiculaires a été mesuré. Des différences significatives d'éclosion suicide entre différents sols ont été obtenues, mais avec un taux d'éclosion élevé. Ces travaux fournissent des éléments clés pour l’utilisation d’exsu
... Останніми роками дослідження генетикопопуляційних процесів для різних видів нематод активно проводиться з використанням мікросателітних маркерів, але їх апробація для фітопаразитичних нематод тривалий час була обмежена всього кількома видами, в тому числіпредставниками родини Globodera, які відомі в якості небезпечних патогенів рослин і мають карантинний статус для більшості країн світу [1][2][3][4][5]. ...
... Цей висновок був підтверджений наступними дослідженнями, проведеними для популяцій блідої глободери з центру походження виду -Перу: виявлений ступінь алельного поліморфізму та варіабельність алельних частот 8 мікросателітних локусів вказували на дефіцит гетерозигот для більшості локусів та відсутність генетичної диференціації для вибірок нематод з популяцій не лише одного поля, а навіть одного регіону. Таким чином, вперше особливості репродукційної моделі глободер були підтверджені на генетичному рівні (інбридинг нащадків через обмежену міграційну здатність інвазійних личинок та самців, внаслідок чого спостерігається дефіцит гетерозиготних генотипів), тоді як відсутність генетичної диференціації для популяцій картопляних глободер з одного регіону вказувала на існуючий у межах регіону потік генів через поширення цист нематод природним шляхом (з вітром, дощем, дикими тваринами), або разом з людською діяльністю (обмін зараженим посадковим матеріалом, використання недезінфікованого спорядження тощо) [2,3]. Оскільки одержані результати збігалися з такими для H. schachtii [2], було висловлено припущення щодо єдиної схеми генетичної диференціації популяцій для всіх видів цистоутворюючих нематод [1]. ...
... Як уже зазначалось, аналогічний тренд щодо дефіциту гетерозиготних генотипів був показаний для G. pallida з популяцій Південної Америки [2,3], і навіть для іншого виду цистоутворюючих нематод -H. schachtii, для якого цей показник становив у середньому 28 % [8]. ...
... Our case study involved the cyst nematode Globodera pallida, one of the major pest of potato crop worldwide (Oerke, Dehne, Schönbeck, & Weber, 2012;Turner & Evans, 1998) from the Andean region of South-America, the origin of its wild host potatoes and other Solanum species (Evans & Stone, 1977;Hijmans & Spooner, 2001). Its main range lies in Peru where Picard, Sempere, and Plantard (2007) highlighted five distinct genetic clades with a south-to-north pattern associated with a decreasing genetic diversity. G. pallida is a sedentary endoparasite. ...
... Moreover, regarding the nematode population effect, there was no impact of G. pallida genetic clades (Picard et al., 2007) on the hatching of juveniles. This result could be due to a differential adaptation of each G. pallida population to contrasted local climate conditions (i.e., temperature, humidity). ...
... Désirée in a greenhouse, were used in this study. These G. pallida populations are members of the genetic clades described byPicard et al. (2007): clade I (P308-Arapa, P299-Amantani 2 and P320-Colca canyon), clade II (P240-Cusco 2 and P252-Cusco 3), clade III (P212-Andahuaylas 4, P214-Andahuaylas 2 and P233-Abancay), clade IV (P323-Huancavelica), ...
Plant–parasite coevolution has generated much interest and studies to understand and manage diseases in agriculture. Such a reciprocal evolutionary process could lead to a pattern of local adaptation between plants and parasites. Based on the phylogeography of each partner, the present study tested the hypothesis of local adaptation between the potato cyst nematode Globodera pallida and wild potatoes in Peru. The measured fitness trait was the hatching of cysts which is induced by host root exudates. Using a cross‐hatching assay between 13 populations of G. pallida and root exudates from 12 wild potatoes, our results did not show a strong pattern of local adaptation of the parasite but the sympatric combinations induced better hatching of cysts than allopatric combinations, and there was a negative relationship between the hatching percentage and the geographical distance between nematode populations and wild potatoes. Moreover, a strong effect of the geographic origin of root exudates was found, with root exudates from south of Peru inducing better hatching than root exudates from north of Peru. These results could be useful to develop new biocontrol products or potato cultivars to limit damages caused by G. pallida.
... The question of whether G. pallida should be considered a species complex rather than a single species has been raised by several authors (Madani et al., 2010;Subbotin, Prado Vera, Mundo-Ocampo, & Baldwin, 2011). Interestingly, previous investigations carried out on G. pallida populations sampled along the Andean Cordillera in Peru have revealed a phylogeographic pattern from south to north, with five distinct clades (named I-V) (Picard, Sempere, & Plantard, 2007), and high nucleotide divergence (10%-11% based on cytochrome B sequencing) between populations belonging to the southern and northern clades (Picard et al., 2007). This first study on the genetic diversity of G. pallida was conducted on a limited population set (44 along a 3000-km transect (Picard et al., 2007;Plantard et al., 2008)), and made use of a set of seven microsatellite loci available at that time. ...
... The question of whether G. pallida should be considered a species complex rather than a single species has been raised by several authors (Madani et al., 2010;Subbotin, Prado Vera, Mundo-Ocampo, & Baldwin, 2011). Interestingly, previous investigations carried out on G. pallida populations sampled along the Andean Cordillera in Peru have revealed a phylogeographic pattern from south to north, with five distinct clades (named I-V) (Picard, Sempere, & Plantard, 2007), and high nucleotide divergence (10%-11% based on cytochrome B sequencing) between populations belonging to the southern and northern clades (Picard et al., 2007). This first study on the genetic diversity of G. pallida was conducted on a limited population set (44 along a 3000-km transect (Picard et al., 2007;Plantard et al., 2008)), and made use of a set of seven microsatellite loci available at that time. ...
... Interestingly, previous investigations carried out on G. pallida populations sampled along the Andean Cordillera in Peru have revealed a phylogeographic pattern from south to north, with five distinct clades (named I-V) (Picard, Sempere, & Plantard, 2007), and high nucleotide divergence (10%-11% based on cytochrome B sequencing) between populations belonging to the southern and northern clades (Picard et al., 2007). This first study on the genetic diversity of G. pallida was conducted on a limited population set (44 along a 3000-km transect (Picard et al., 2007;Plantard et al., 2008)), and made use of a set of seven microsatellite loci available at that time. Since then, novel microsatellite loci have been developed directly from G. pallida genome (Cotton et al., 2014), selected and combined together to develop a new robust genotyping tool based on 13 microsatellite loci (Montarry et al., 2019(Montarry et al., , 2015. ...
Our knowledge of the diversity of potato cyst nematodes in their native areas still remains patchy and should be improved. A previous study based on 42 Peruvian Globodera pallida populations revealed a clear south to north phylogeographic pattern, with five well‐supported clades and maximum diversity observed in the south of Peru. In order to investigate this phylogeographic pattern more closely, we genotyped a larger collection of Peruvian populations using both cathepsin L gene sequence data and a new set of 13 microsatellite loci. Using different genetic analyses (STRUCTURE, DAPC), we consistently obtained the same results that led to similar conclusions: the presence of a larger genetic diversity than previously known suggesting the presence of cryptic species in the south of Peru. These investigations also allowed us to clarify the geographic borders of the previously described G. pallida genetic clades, and to update our knowledge of the genetic structure of this species in its native area, with the presence of additional clades. A distance‐based redundancy analysis (dbRDA) was also carried to understand whether there was a correlation between the population genetic differentiation and environmental conditions. This analysis showed that genetic distances observed between G. pallida populations are explained firstly by geographic distances, but also by climatic and soil conditions. This work could lead to a revision of the taxonomy that may have strong implications for risk assessment and management, especially on a quarantine species.
... PCR-ITS-RFLP, conventional PCR and Real-Time PCR with species-specific primers and ITS-rRNA and mtDNA gene sequence analysis have been developed and are now becoming useful tools for identification of Globodera species . The analyses of South American populations of G. pallida revealed high levels of genetic diversity among them (Picard et al., 2007 and, consequently, Grenier et al. (2010) noted the importance of evaluating available molecular diagnostic tools in relation to the new understanding of the wider diversity in South American populations. It has been shown that the populations of PCN from South America have a different genetic composition from those in Europe. ...
... The availability of molecular data for Globodera had a significant impact on the systematics of this group, reshaping concepts of its species relationships and origins. Distinct genetic differences among G. pallida populations spanning Europe and other regions and those found in South America were revealed by sequence and phylogenetic analyses of the ITS-rRNA (Blok et al., 1998;Subbotin et al., 2000Subbotin et al., , 2011Madani et al., 2010;Skantar et al., 2011;Hoolahan et al., 2012a), cytb (Picard et al., 2007Plantard et al., 2008;Pylypenko et al., 2008;Madani et al., 2010;Geric Stare et al., 2013) and COI (Chitambo et al., 2019) genes. The analysis of partial cytb gene sequences and microsatellites of G. pallida collected in different regions allowed the identification of the origin of western European populations with a high degree of certainty (Picard et al., 2007Plantard et al., 2008). ...
... Distinct genetic differences among G. pallida populations spanning Europe and other regions and those found in South America were revealed by sequence and phylogenetic analyses of the ITS-rRNA (Blok et al., 1998;Subbotin et al., 2000Subbotin et al., , 2011Madani et al., 2010;Skantar et al., 2011;Hoolahan et al., 2012a), cytb (Picard et al., 2007Plantard et al., 2008;Pylypenko et al., 2008;Madani et al., 2010;Geric Stare et al., 2013) and COI (Chitambo et al., 2019) genes. The analysis of partial cytb gene sequences and microsatellites of G. pallida collected in different regions allowed the identification of the origin of western European populations with a high degree of certainty (Picard et al., 2007Plantard et al., 2008). These analyses showed that all these populations originated from a single restricted area in the extreme south of Peru, located between the north shore of the Lake Titicaca and Cusco. ...
Globodera presently contains 13 valid and three as yet undescribed species. Three species, G. rostochiensis, G. pallida and G. ellingtonae, the potato cyst nematodes (PCN), cause significant economic losses on potatoes around the world. In our study we provide comprehensive phylogenetic analyses of 455 ITS rRNA, 219 COI and 164 cytb gene sequences of 11 valid and two undescribed species of Globodera using Bayesian inference, maximum likelihood and statistical parsimony. New 205 COI, 116 cytb and 21 ITS rRNA gene sequences were obtained from 148 populations of these species collected from 23 countries. The phylogenetic analysis revealed that Globodera displayed two main clades in the trees: i) Globodera from South and North America parasitising plants from Solanaceae; and ii) Globodera from Africa, Europe, Asia and New Zealand parasitising plants from Asteraceae and other families. Based on the results of phylogeographical analysis and age estimation of clades with a molecular clock approach, it is hypothesised that Globodera species originated and diversified from several centres of speciation located in mountain regions and then dispersed across the world from these regions during the Pleistocene. High genetic diversity of Bolivian populations of G. rostochiensis was observed for both mtDNA genes. Analysis of phylogenetic relationships of G. pallida and G. rostochiensis populations revealed incongruence in topology between networks inferred from mtDNA genes, which might be an indication of possible recombination and selective introgression events through gene flow between previously isolated populations. This puts some limitations on the use of the mtDNA marker as universal DNA barcoding identifier for PCN. Globodera bravoae syn. n. is proposed as a junior synonym of G. mexicana.
... G. pallida and nematodes ascribed to G. "mexicana" form a monophyletic clade, whereas G. rostochiensis and G. tabacum form its sister monophyletic clade ( Fig. 4; Subbotin et al., 2000Subbotin et al., , 2001Subbotin et al., , 2004bPicard et al., 2007). G. "mexicana" is in fact a poorly known species whose individuals analysed here were sampled in Mexico, where it parasites wild members of Solanaceae (Thiéry et al., 1997); however this taxon is likely to have dispersed from South America to Central America along with members of Solanaceae following the Pliocene establishment of the Panamanian land bridge. ...
... Such high levels of sequence divergence point to N1 Myr evolutionary times, in contrast with the b0.001 Ma age of potato domestication (Picard et al., 2007). Each G. pallida lineage must therefore have independently infected cultivated potatoes in its respective area during the last millennia. ...
... The same south-to-north pattern is also observed for allelic richness using (nuclear) microsatellite markers (Picard et al., 2007). The allelic richness is nearly twice in the south than in the north. ...
Physical paleoaltimetric methods are increasingly used to estimate the amount and timing of surface uplift in orogens. Because the rise of mountains creates new ecosystems and triggers evolutionary changes, biological data may also be used to assess the development and timing of regional surface uplift. Here we apply this idea to the Peruvian Andes through a molecular phylogeographic and phylochronologic analysis of Globodera pallida, a potato parasite nematode that requires cool temperatures and thus thrives above 2.0–2.5 km in these tropical highlands. The Peruvian populations of this species exhibit a clear evolutionary pattern with deeper, more ancient lineages occurring in Andean southern Peru and shallower, younger lineages occurring progressively northwards. Genetically diverging G. pallida populations thus progressively colonized highland areas as these were expanding northwards, demonstrating that altitude in the Peruvian Andes was acquired longitudinally from south to north, i.e. in the direction of decreasing orogenic volume. This phylogeographic structure is recognized in other, independent highland biotaxa, and point to the Central Andean Orocline (CAO) as the region where high altitudes first emerged. Moreover, molecular clocks relative to Andean taxa, including the potato–tomato group, consistently estimate that altitudes high enough to induce biotic radiation were first acquired in the Early Miocene. After calibration by geological and biological tie-points and intervals, the phylogeny of G. pallida is used as a molecular clock, which estimates that the 2.0–2.5 km threshold elevation range was reached in the Early Miocene in southernmost Peru, in the Middle and Late Miocene in the Abancay segment (NW southern Peru), and from the latest Miocene in central and northern Peru. Although uncertainties attached to phylochronologic ages are significantly larger than those derived from geochronological methods, these results are fairly consistent with coeval geological phenomena along the Peruvian Andes. They strongly suggest that orogenic volume initially developed in the CAO during most of the Miocene until a breakthrough in the latest Miocene allowed the northward propagation of crustal thickening into central and northern Peru, possibly by ductile crustal flow from the CAO. Such a combined phylogeographic and phylochronologic approach to regional uplift opens perspectives to estimate the direction(s) and timing of acquisition of altitude over other Cenozoic orogens.
... Twenty-four initial G. pallida populations, each composed of 100 cysts, were established by mixing four Peruvian populations that are genetically differentiated and show high allelic richness (P83_otuzco1, P252_cusco3, P286_puno1 and P298_amantani2 [53]). These G. pallida populations are members of the genetic clades I (P286_puno1 and P298_amantani2), II (P252_cusco3) and V (P83_otuzco1) described by Picard et al. [53] and have all been multiplied on the susceptible potato cultivar Désirée. ...
... Twenty-four initial G. pallida populations, each composed of 100 cysts, were established by mixing four Peruvian populations that are genetically differentiated and show high allelic richness (P83_otuzco1, P252_cusco3, P286_puno1 and P298_amantani2 [53]). These G. pallida populations are members of the genetic clades I (P286_puno1 and P298_amantani2), II (P252_cusco3) and V (P83_otuzco1) described by Picard et al. [53] and have all been multiplied on the susceptible potato cultivar Désirée. Before mixing these populations, the number of larvae was scored using a magnifying stereomicroscope for 12 randomly chosen cysts which were individually crushed in water, and a one-way ANOVA showed no significant difference in the number of larvae per cyst between those four populations (F 3,44 ¼ 1.59; p ¼ 0.21; figure 1). ...
The effective size of a population is the size of an ideal population which would undergo genetic drift at the same rate as the real population. The balance between selection and genetic drift depends on the effective population size (N e ), rather than the real numbers of individuals in the population (N). The objectives of the present study were to estimate N e in the potato cyst nematode Globodera pallida and to explore the causes of a low N e /N ratio in cyst nematodes using artificial populations. Using a temporal analysis of 24 independent populations, the median N e was 58 individuals (min N e ¼ 25 and max N e ¼ 228). N e is commonly lower than N but in the case of cyst nematodes, the N e /N ratio was extremely low. Using artificial populations showed that this low ratio did not result from migration, selection and overlapping generations, but could be explain by the fact that G. pallida populations deviate in structure from the assumptions of the ideal population by having unequal sex ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a low N e , resulting in a strong intensity of genetic drift, could be important for their control because G. pallida populations will have a low capacity to adapt to changing environments. © 2019 The Author(s) Published by the Royal Society. All rights reserved.
... The centre of origin of both species is the Andes mountains in South America (Evans and Stone, 1977). A study revealed five distinct clades (Picard et al., 2007) of a Peruvian population of G. pallida using two molecular marker systems (partial sequence of the mitochondrial gene cytochrome b and microsatellite loci) with its colonization from South to North. When Peruvian populations from these clades were exposed to various potato resistance genes they exhibited large differences in virulence. ...
... Peruvian PCN populations were classified into five clades Vm, IVm, IIIm, IIn and Im (Picard et al., 2007), while Western European populations fell into two groups only. One group corresponded to clade Im and included all European populations, the other comprised the remaining Northern clades (Plantard et al., 2008). ...
Potato cyst nematode (PCN) species, Globodera pallida (white cyst nematode) and Globodera rostochiensis (golden cyst nematode) cause serious yield losses to the potato crop worldwide. Several cultivated Solanum (Group tuberosum) and wild potato species possess R genes and QTL for resistance against PCN. R-genes like H1and Gpa5 confer a high level of resistance to G. rostochiensis pathotypes Rol and Ro4 and G. pallida pathotypes Pa2 and Pa3, respectively. Several PCN resistant potato cultivars that are grown worldwide have been bred involving the H1 gene. With the development of DNA marker technology linkage maps were constructed to map loci involved in resistance to different pathotypes of PCN. Mapping these loci led to the development of molecular markers to screen segregating populations for resistance to PCN in the absence of the pathogen. Markers linked to R genes and resistance QTL have potential for making tailor made varieties through marker-assisted selection (MAS). This article presents an update on resistance sources available in major worldwide gene banks, R genes, QTLs and molecular markers for PCN resistance.
... They showed that durability in European cultivars would only persist if there was no threat from new virulence genes arising in European populations of the nematode, a view supported by Grenier et al. (2010). Picard et al. (2007), studying populations of G. pallida in Peru, also illustrated the potential for genetic divergence among populations on cultivated plants, and recent research in plant host/nematode interactions refers to a G. pallida virulence factor, Gp-Rbp-1 (Sacco et al., 2009). Such evidence illustrates the potential risk to European potato production associated with introducing new virulent strains from outside Europe and particularly South America. ...
... PCN is an internationally regulated pest, and the risk posed to European potato production by introducing an increased genetic diversity from other parts of the world cannot be underestimated. Despite the diversity of virulence among European populations of PCN, there is clearly much greater genomic diversity that exists elsewhere (Bendezu et al., 1998;Picard et al., 2007;Plantard et al., 2008). It is justified to assume that this greater molecular diversity also reflects a greater diversity of virulence, first reported over 30 years ago (Canto Saenz & de Scurrah, 1977;Kort et al., 1977). ...
The potato cyst nematodes Globodera pallida and G. rostochiensis are listed in the EU Plant Health Directive 2000/29/EC and are also subject to the new EU Council Directive 2007/33/EC on the control of potato cyst nematodes, requiring unilateral suppression of these pests in Europe. At the same time there is also pressure to increase world trade in potatoes. Such pressure has to be balanced by the risks involved in the associated spread of these pests and subsequent problems in management. Populations of the potato cyst nematodes from outside Europe, in particular South America, which is considered the origin of G. pallida and G. rostochiensis, pose a risk to those European countries where limited genetic variability of these nematode species has been recorded. The development and usage of resistant cultivars under such conditions has formed a pivotal role in integrated management programmes in Europe. Molecular studies have shown that populations of G. pallida and G. rostochiensis from South America have a different genetic composition from those in Europe. The introduction of such populations would pose a threat to the use of resistant cultivars as a major tool in reducing the potential spread and damage caused by these species. At present, an inability to link precisely genetic variability to the virulence characteristics of a specific nematode population, and quickly identify the virulence status of intercepted populations for inspection purposes, strengthens the case for using plant health legislation to prevent their introduction.
... Due to a high copy number in individual cells, lack of recombination and strict maternal inheritance, mitochondrial genes (mtDNA) can also be used as excellent markers in addition to the ITS rRNA for diagnostics and the study of phylogenetic relationships. Recently, mtDNA has been used to study genetic relationships among Peruvian populations of G. pallida and to identify the origin of Western European populations of this species (Picard et al., 2007;Plantard et al., 2008). Using mtDNA gene, cytochrome b (cytb) sequences, Plantard et al. (2008) showed that G. pallida presently distributed in Europe was derived from a single restricted area in the extreme south of Peru, located between the north shore of the Lake Titicaca and Cusco. ...
... Distinct genetic differences between European populations and South American populations belonging to the P5A pathotype (Phillips & Trudgill, 1998) of G. pallida were revealed by ITS-rRNA (Blok et al., 1998;Subbotin et al., 2000;present study) and cytb (Picard et al., 2007;Plantard et al., 2008;Pylypenko et al., 2008;present study) sequences and phylogenetic analyses, simple sequence repeat primer analysis (Blok & Phillips, 1995), PCR-RAPD (Blok et al., 1997;Bendezu et al., 1988;Grenier et al., 2001;Rumpenhorst & Ayub, 2001), IEF of proteins (Rumpenhorst & Ayub, 2001), 2-DGE of proteins (Grenier et al., 2001), and satellite DNA analysis (Grenier et al., 2001). The sequence and phylogenetic analyses of Globodera species parasitizing solanaceous plants made by Subbotin et al. (2000) indicated the presence of a separate group of populations closely related to G. pallida, which might represent an undescribed Globodera species. ...
The mitochondrial cytochrome b gene (cytb), the internal transcribed spacer region (ITS1-5.8S-ITS2) of the rRNA gene and D2-D3 expansion segments of the 28S rRNA gene were amplified, sequenced and used to characterize several populations of potato cyst nematodes, Globodera pallida and G. rostochiensis, collected from different areas in Canada. Diagnostic PCR-ITS-RFLP profiles with three restriction enzymes are provided for identification of both species. Sequences of ITS rRNA and cytb genes were compared with those in Genbank of other potato cyst nematode populations originating from Europe, South America, USA, Australia and New Zealand. The ITS rRNA sequences of Canadian G. rostochiensis were similar to those of all previously sequenced populations of this species. Sequence divergence of ITS rRNA for G. rostochiensis varied from 0 to 1.6%, whereas for G. pallida sequence divergence among populations reached 1.95%. Sequence and phylogenetic analysis of cytb and ITS rRNA genes using Bayesian inference revealed that Canadian G. pallida is almost identical to European and USA populations and formed a large clade with all these populations on the phylogenetic trees. The present molecular result with cytb confirmed the hypothesis that there are possibly several sibling species within G. pallida. Our study also supports a previously proposed hypothesis regarding introduction of G. pallida from a restricted area in Peru, firstly into Europe with subsequent spread to other continents including North America. Our sequence analysis revealed that several newly obtained sequences cannot be translated into functional cytb protein, because point indels disrupt the reading frame. Poly(T) variation in mtDNA genes in G. pallida might be explained by post-transcriptional editing mechanisms in Globodera mitochondria as well as by errors during PCR amplification of mononucleotide repeats within these genes.
... In Venezuela, G. pallida Pa4 and Pa5 are the most dominant. Interestingly, mitochondrial DNA studies showed a genetic relationship between the Peruvian populations of G. pallida and European populations (Picard et al., 2007;Plantard et al., 2008;Subbotin et al., 2019). G. rostochiensis is native to Bolivia, Chile, Colombia, Ecuador, Peru and Venezuela, while G. pallida is only native to Bolivia (Table 2). ...
Potato Cyst Nematode(s) is one of a series of case studies, sponsored by the British Society for Plant Pathology, on damaging plant diseases which continue to have major economic, social and environmental impacts around the world. The case studies provide an historical overview of responses and reactions to plant pandemics, from control and regulation to research and beyond. The purpose of this and other reports in the series is to raise awareness of plant pandemics and to stimulate wider interest in their consequences for all, including current and future researchers. Copies of the report are available from the BSPP | www.bspp.org.uk.
... Molecular techniques are recommended in European and Mediterranean Plant Protection Organization (EPPO) for routine testing [16]. In recent years, PCR-based methods have been reported for identification and diagnosis of G. rostochiensis using conventional PCR [17][18][19][20][21], and TaqMan real-time PCR [22][23][24][25]. DNA barcoding based on cytochrome c oxidase subunit I (COI), 18S rDNA, and 28S rDNA can support the identification of G. rostochiensis [26]. ...
Globodera rostochiensis is an important quarantine pest, it causes serious potato yield losses annually. Reliable and rapid molecular detection of G. rostochiensis is pivotal to effective early disease diagnosis and managements. Herein, recombinase polymerase amplification integrated with lateral flow assays method (RPA-LFA) was developed to target the internal transcribed spacer of nuclear ribosomal DNA (ITS rDNA) of the golden cyst nematode (G. rostochiensis), which allowed for the rapid diagnosis and detection of this nematode from crude extracts of cysts and juveniles within 30 min. Sensitivity test results showed that 10−1 single juvenile and 10−3 single cyst can be reliably detected. Moreover, the RPA-LFA method can directly diagnose and detect G. rostochiensis from infested field soil. This is the first RPA-LFA method for diagnosis G. rostochiensis, it is a fast, accurate, and sensitive detection method and can be developed for detection of G. rostochiensis in fields and laboratories lacking large instrument and equipment.
... PCN co-evolved with their hosts from the genus Solanum in South America (Canto Saenz and Mayer de Scurrah, 1977;Stone, 1985). For G. pallida, this co-evolution is estimated to have taken place over 20 million years, with a northward expansion from the south of Peru around Lake Titicaca (Picard et al., 2004(Picard et al., , 2007. Both nematode species were probably introduced and became established in Europe in the 1850s as a consequence of the Irish potato famine (Evans et al., 1975), when tubers, with contaminated soil attached, were collected and brought to Europe as breeding material for late blight resistant potatoes. ...
Potato cyst nematodes (PCN) are economically important pests with a worldwide distribution in all temperate regions where potatoes are grown. Because above ground symptoms are non-specific, and detection of cysts in the soil is determined by the intensity of sampling, infestations are frequently spread before they are recognised. PCN cysts are resilient and persistent; their cargo of eggs can remain viable for over two decades, and thus once introduced PCN are very difficult to eradicate. Various control methods have been proposed, with resistant varieties being a key environmentally friendly and effective component of an integrated management programme. Wild and landrace relatives of cultivated potato have provided a source of PCN resistance genes that have been used in breeding programmes with varying levels of success. Producing a PCN resistant variety requires concerted effort over many years before it reaches what can be the biggest hurdle—commercial acceptance. Recent advances in potato genomics have provided tools to rapidly map resistance genes and to develop molecular markers to aid selection during breeding. This review will focus on the translation of these opportunities into durably PCN resistant varieties.
... There have been many phylogenetic analyses of species within the genus Globodera (e.g., [5,73,[76][77][78][79][80][81][82][83][84][85][86]). A recent study, based on a phylogenetic analysis of gene sequences of three molecular markers (455 ITS rRNA, 219 COI, and 164 cytb) of 11 valid and 2 undescribed species of Globodera [87], found that Globodera displayed two main clades in their phylogenetic trees: (i) Globodera from South and North America parasitizing plants from Solanaceae; and (ii) Globodera from Africa, Europe, Asia, and New Zealand parasitizing plants from Asteraceae and other families. ...
The scope of this paper is limited to the taxonomy, detection, and reliable morphological and molecular identification of the potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis. It describes the nomenclature, hosts, life cycle, pathotypes, and symptoms of the two species. It also provides detailed instructions for soil sampling and extraction of cysts from soil. The primary focus of the paper is the presentation of accurate and effective methods to identify the two principal PCN species.
... This was unexpected as this plant has not previously been listed in G. pallida's host range, and more so, the Brassicaceae are phylogenetically far from Solanaceae. These results raised the questions whether all broccoli varieties have this ability and whether hatching is stimulated at the same level for all populations of G. pallida [i.e., European population and South American populations belonging to the 5 clades described by Picard et al. (2007)]. These results revealed that, it might be possible to identify non-host plants that can induce substantial hatching and that it may be interesting to screen outside the referenced host range for future use as cash and/or trap crops. ...
Cyst nematodes account for substantial annual yield losses in crop production worldwide. Concerns over environmental and health issues due to the use of chemical nematicides mean alternative sustainable and integrated solutions are urgently required. Hatch induction of encysted eggs in the absence of host plants, i.e., ‘suicide-hatching,’ could be a sustainable alternative in reducing population densities of cyst nematodes in infested soils. Here we examined in situ hatching of encysted eggs of Globodera pallida, Heterodera carotae, and Heterodera schachtii at varying soil depths, following exogenous applications of host root exudates in repeated glasshouse experiments. Cysts were retrieved 30 or 43 days post-incubation depending on the nematode species and assessed for hatching rates relative to the initial number of viable eggs per cyst. Hatching of the potato cyst nematode G. pallida depended on both soil moisture and effective exposure to root exudates, and to a lesser extent on exudate concentration. The carrot cyst nematode H. carotae had over 75% hatched induced by root exudate irrespective of the concentration, with better hatch induction at 20 cm as compared with 10 cm soil depth. Hatching of the beet cyst nematode H. schachtii largely depended on the soil moisture level at constant temperature, rather than the type or concentration of root exudates applied. As a conclusion, exogenously applied host root exudates may play a major role in inducing in situ hatch of encysted eggs of potato and carrot cyst nematodes in the absence of host plant under favorable soil temperature/moisture conditions. To improve such strategy, the characterization of chemical profiles of the root exudate composition and field validation are currently ongoing.
... Both PCN species originate from South America and were likely brought into Europe during the 19th century [6,15]. Based on microsatellite and mitochondrial cytochrome b sequence analyses [16], several distinct introductions of G. pallida from different regions in Southern Peru into Europe (including the UK) seem to have occurred; by contrast, the G. rostochiensis present in the UK appears to have been derived from a more restricted introduction. The complex nature of the UK G. pallida populations [17] makes their control using host resistance potentially challenging as no single major R gene is likely to be effective and remain durable against the diversity of G. pallida present in Europe. ...
Although the use of natural resistance is the most effective management approach against the potato cyst nematode (PCN) Globodera pallida, the existence of pathotypes with different virulence characteristics constitutes a constraint towards this goal. Two resistance sources, GpaV (from Solanum vernei) and H3 from S. tuberosum ssp. andigena CPC2802 (from the Commonwealth Potato Collection) are widely used in potato breeding programmes in European potato industry. However, the use of resistant cultivars may drive strong selection towards virulence, which allows the increase in frequency of virulent alleles in the population and therefore, the emergence of highly virulent nematode lineages. This study aimed to identify Avirulence (Avr) genes in G. pallida populations selected for virulence on the above resistance sources, and the genomic impact of selection processes on the nematode. The selection drive in the populations was found to be specific to their genetic background. At the genomic level, 11 genes were found that represent candidate Avr genes. Most of the variant calls determining selection were associated with H3-selected populations, while many of them seem to be organised in genomic islands facilitating selection evolution. These phenotypic and genomic findings combined with histological studies performed revealed potential mechanisms underlying selection in G. pallida.
... Microsatellites may be valuable for population genetic structure and progeny analyses in Globodera species (Thiéry and Mugniéry 2000). In Globodera pallida, microsatellites have previously been used successfully to investigate the origin of the European populations of this pest (Plantard et al. 2008), and to reveal the phylogeographical history and reduction of the allelic richness of Peruvian G. pallida populations (Picard et al. 2007). Microsatellite markers have also been developed for G. rostochiensis to reveal the phylogeographical history of G. rostochiensis populations in Canada (Boucher et al. 2013). ...
Global trading of plant materials, in combination with agricultural practices, may facilitate the spreading of cyst nematodes to so far non-infected areas. Recently Potato Cyst Nematode (PCN) was recognized to be present in Indonesia and both diversity and distribution require further study. Assessment of PCN populations was done by collecting soil samples, determination of morphological characteristics in combination with ITS rDNA and COI mtDNA sequencing. Thirty-seven soil samples were collected from potato fields in the Indonesia archipelago. The results showed the presence of Globodera rostochiensis in 22 out of 37 sampling fields, namely North Sumatra (6 fields), Central Java (12 fields), East Java (3 fields), and -for the first time- in Sulawesi (North Sulawesi) (1 field). The highest observed density was found in Banjarnegara (Central Java), i.e., 872 cysts 100 ml soil−1. Globodera pallida was not recovered. Both ITS and COI characterisation of Indonesian PCN (G. rostochiensis) revealed the virtual absence of sequence variation as compared to most PCN from the rest of the world; the COI sequences were identical to the most common and mostly distributed haplotype around the world. Microsatellite genotyping indicated a higher genetic diversity for populations from East Java than for populations from North Sumatra, suggesting that cysts at the origin of populations in North Sumatra were coming from populations in East Java. These data on species identification, population density, genetic diversity, and distribution of potato cyst nematode over the Indonesian archipelago constitute the very basis for the design of environmentally-sound and effective PCN control strategies.
... 42 . Nevertheless, diversity values are much lower than in the amphimictic species G. pallida, which showed 12% CytB divergence among native Peruvian clades associated with relatively high levels of diversity and gene flow 43 . ...
The soil-borne nematode Xiphinema index is closely linked to its main host, the grapevine, and presents a major threat to vineyards worldwide due to its ability to transmit Grapevine fanleaf virus (GFLV). The phylogeography of X. index has been studied using mitochondrial and microsatellite markers in samples from most regions of its worldwide distribution to reveal its genetic diversity. We first used the mitochondrial marker CytB and illustrated the low intraspecific divergence of this mainly meiotic parthenogenetic species. To generate a higher polymorphism level, we then concatenated the sequences of CytB and three mitochondrial markers, ATP6, CO1 and ND4, to obtain a 3044-bp fragment. We differentiated two clades, which each contained two well-supported subclades. Samples from the eastern Mediterranean and the Near and Middle East were grouped into three of these subclades, whereas the samples from the western Mediterranean, Europe and the Americas all belonged to the fourth subclade. The highest polymorphism level was found in the samples of one of the Middle and Near East subclades, strongly suggesting that this region contained the native area of the nematode. An east-to-west nematode dissemination hypothesis appeared to match the routes of the domesticated grapevine during Antiquity, presumably mainly dispersed by the Greeks and the Romans. Surprisingly, the samples of the western subclade comprised only two highly similar mitochondrial haplotypes. The first haplotype, from southern Iberian Peninsula, Bordeaux and Provence vineyards, exhibited a high microsatellite polymorphism level that suggests introductions dating from Antiquity. The second haplotype contained a highly predominant microsatellite genotype widespread in distant western countries that may be a consequence of the massive grapevine replanting following the 19th-century phylloxera crisis. Finally, our study enabled us to draw a first scaffold of X. index diversity at the global scale.
... The genetic structure and the evolutionary history of several cyst nematodes have been previously studied at different spatial scales, e.g. the potato cyst nematodes Globodera pallida (Eves-van den Akker et al., 2015;Picard et al., 2004;Picard et al., 2007;Plantard et al., 2008) and G. rostochiensis (Boucher et al., 2013;Mimee et al., 2015), the tobacco cyst nematode G. tabacum (Alenda et al., 2014;Marché et al., 2001), the beet cyst nematode Heterodera schachtii (Kim et al., 2018;Plantard and Porte, 2004), the cereal cyst nematode H. avenae (Wang et al., 2018) or the soybean cyst nematode H. glycines (St-Marseille et al., 2018;Wang et al., 2015). However, to our knowledge, no study has been conducted to describe the genetic structure of the carrot cyst nematode Heterodera carotae, except two recent studies using genic markers with a diagnostic purpose (Escobar-Avila et al., 2018;Madani et al., 2017). ...
The cyst nematode Heterodera carotae, which parasitizes carrot roots, has been recorded in many countries in Europe (Italy, The Netherlands, Switzerland, France, Denmark, …), in South Africa and in North America (Canada, USA). To date, there is a lack of knowledge about the genetic structure of the populations of this economically important nematode. The aim of this work was to study the structuration of the genetic diversity of the carrot cyst nematode at the European scale. We have developed a set of thirteen polymorphic microsatellite markers and used it to genotype seventeen European populations of H. carotae coming from France, Switzerland, Italy, Denmark and one non-European population from Canada. As previously showed for other cyst nematode species, the H. carotae populations were characterised by a strong heterozygote deficit. A Bayesian clustering analysis revealed two distinct genetic clusters, with one group located in the north of Europe and a second one located in the south of Europe. Moreover, our results highlighted rather limited gene flow at small spatial scale and some events of long distance migration. This first investigation of the genetic diversity of H. carotae populations would be useful to develop sustainable control strategies.
... which indicates a long process of coevolution between the nematodes and their hosts. Indeed, it has been speculated that the Incas introduced 6-8 years potato crop rotation in South America to mitigate PCN (Picard et al. 2007). Several distinct pathotypes (subpopulations) have been reported for G. rostochiensis and G. pallida that are differentiated based on their ability to infect Solanum ssp. ...
Key message
The nematode resistance gene H2 was mapped to the distal end of chromosome 5 in tetraploid potato.
Abstract
The H2 resistance gene, introduced into cultivated potatoes from the wild diploid species Solanum multidissectum, confers a high level of resistance to the Pa1 pathotype of the potato cyst nematode Globodera pallida. A cross between tetraploid H2-containing breeding clone P55/7 and susceptible potato variety Picasso yielded an F1 population that segregated approximately 1:1 for the resistance phenotype, which is consistent with a single dominant gene in a simplex configuration. Using genome reduction methodologies RenSeq and GenSeq, the segregating F1 population enabled the genetic characterisation of the resistance through a bulked segregant analysis. A diagnostic RenSeq analysis of the parents confirmed that the resistance in P55/7 cannot be explained by previously characterised resistance genes. Only the variety Picasso contained functionally characterised disease resistance genes Rpi-R1, Rpi-R3a, Rpi-R3b variant, Gpa2 and Rx, which was independently confirmed through effector vacuum infiltration assays. RenSeq and GenSeq independently identified sequence polymorphisms linked to the H2 resistance on the top end of potato chromosome 5. Allele-specific KASP markers further defined the locus containing the H2 gene to a 4.7 Mb interval on the distal short arm of potato chromosome 5 and to positions that correspond to 1.4 MB and 6.1 MB in the potato reference genome.
... ITS-rDNA fragment amplification was performed using the TW81 and AB28 primers as described by Joyce et al. (1994). Two specific primers for G. pallida cytochrome b were used to amplify an 872 bp fragment as described by Picard et al. (2007). The PCR products were loaded on a 1% agarose gel, separated by electrophoresis, and visualised by ethidium bromide staining and UV illumination. ...
The aim of the present study was to evaluate the geographical distribution, infestation degree, and diversity of Potato Cysts Nematode (PCN) in Algeria, including the southern regions. Accurate identification of PCN is essential to determine the appropriate control methods to be used in an Integrated Pest Management program. PCNs were found in forty percent (12 out of thirty) of localities sampled. The average population density of PCN was much higher in the southern regions, compared to the northern regions (9.8 cysts per 100 cm3 vs.4.6 cysts per 100 cm3). The southern potato production areas were more infested with PCN than those of the north (7 from 25 fields in North vs. 5 from 5 fields in the South). Globodera pallida occurred predominantly in the northern region of Algeria, whereas G. rostochiensis occurred predominantly in the southern regions. No mixtures of these species were found in any of the positive studied localities. These species were confirmed by the molecular analysis based on PCR with species-specific primers, ITS-rDNA, and cytochrome b of mtDNA. The low molecular diversity and their phylogenetic association with the European populations of PCN suggest that Algerian populations were probably introduced from Europe, probably by infested seed-potato.
... The ribosomal DNA sequences (rDNA) including two ITS and 5.8S ribosomal RNA were amplified using the primers of Ferris et al. (1995): forward (CGT AAC AAG GTA GCT GTA GC) and reverse (TCC TCC GCT AAA TGA TAT G). Partial sequences of the mitochondrial cytochrome b gene (cytb) were amplified using primers INRAcytbL (GGG TGT GGC CTT GTT ATT TC) and INRAcytbR (AGG ATG GGG TTT TAG CTG GT) (Picard et al. 2007). The 25 µL reaction mixture contained 0.5 U KOD Neo Plus polymerase (Toyobo, Tokyo, Japan), 1 × reaction buffer, 1.5 mM MgSO 4 , 0.2 mM dNTPs, 0.3 µM each primer, and 2.5 µL of crude lysate. ...
In Japan, Globodera pallida was first reported in Abashiri city, Hokkaido in 2015. Sequences of ribosomal DNA (rDNA) and mitochondrial cytochrome b gene (cytb) from the Japanese population of G. pallida were compared with those of overseas populations. The representative sequences for rDNA and for cytb from the Japanese population had 100% identity with the sequences from G. pallida populations of North America and Europe in GenBank. Phylogenetic analysis also showed that they clustered in the clade that included populations from Europe and North America. From these results, we concluded that the Japanese population of G. pallida is close to populations that have been reported in Europe and North America. Recent studies suggested that a few populations of G. pallida were introduced into Europe from South America and have spread to various places around the world, and according to our results, into Japan also.
... It is unlikely that the recent G. pallida presence in southern Idaho is associated with new G. pallida entry from outside Idaho. Our assessment is based on previous studies indicating that G. pallida populations differ between themselves generally only in areas throughout Europe and South America where G. pallida has been long-established (based on molecular phylogenetic analysis), suggesting multiple waves of G. pallida entry (Grenier et al. 2010;Picard et al. 2004Picard et al. , 2007Plantard et al. 2008). Using deterministic spatial interpolation techniques, we enumerated the number of G. pallida cysts and the values of egg viability in associated areas close to initial infestation foci. ...
The potato cyst nematode (PCN), Globodera pallida, is a globally regulated and quarantine potato pest. It was detected for the first time in the U.S. in the state of Idaho in 2006. A spatial analysis was performed to: (i) understand the spatial arrangement of PCN infested fields in southern Idaho using spatial point pattern analysis; and (ii) evaluate the potential threat of PCN for entry to new areas using spatial interpolation techniques. Data point locations, cyst numbers and egg viability values for each infested field were collected by USDA-APHIS during 2006-2014. Results showed the presence of spatially clustered PCN infested fields (P = 0.003). We determined that the spread of PCN grew in diameter from the original center of infestation toward the southwest as an ellipsoidal-shaped cluster. Based on the aggregated spatial pattern of distribution and the low extent level of PCN infested fields in southern Idaho, we determined that PCN spread followed a contagion effect scenario, where nearby infested fields contributed to the infestation of new fields, probably through soil contaminated agricultural equipment or tubers. We determined that the recent PCN presence in southern Idaho is unlikely to be associated with new PCN entry from outside the state of Idaho. The relative aggregation of PCN infested fields, the low number of cysts recovered, and the low values in egg viability facilitate quarantine activities and confine this pest to a small area, which, in 2017, is estimated to be 1,233 hectares. The tools and methods provided in this study should facilitate comprehensive approaches to improve PCN control and eradication programs as well as to raise public awareness about this economically important potato pest.
... The general biogeographical pattern of south-tonorth migration following Andean uplift has been described for several other Andean plants such as Oreobolus R.Br. (Chac on et al., 2006), potatoes and their cyst-nematodes (Picard, Sempere & Plantard, 2007), Perezia Lag. (Simpson et al., 2009), Barnadesioideae (Gruenstaeudl et al., 2009), Azorella Lam. ...
The tropical Andes are a biodiversity hotspot, partly due to their rich and complex floristic composition. A fundamental question regarding this outstanding biodiversity is what role the Andean orogeny has played in species diversification. Ceroxylon is a genus of endemic Andean palms that stands out in the palm family (Arecaceae) due to its adaptation to cold, mountainous environments. Here, we reconstruct the biogeography and climatic preference of this lineage to test the hypothesis that Andean uplift allowed diversification by providing suitable habitats along climatic and elevational gradients. Ancestral areas were reconstructed under a model allowing for founder-event speciation and climatic niches were inferred from climatic variables at present-day occurrences of all species. Niche evolution in a phylogenetic framework was evaluated by testing differences between the climatic niches of clades. Our analyses identified four main clades, with a general pattern of diversification through geographical colonization from south to north after the Pliocene uplift of the northern Andes. Adaptation to low temperatures was conserved at the generic level, with climatic niche differentiation among clades along elevational temperature gradients. We conclude that the Neogene Andean uplift has facilitated the diversification of this iconic plant group via opportunities for geographical migration and separation within its climatic niche.
... In the cyst nematode Globodera pallida, microsatellites have previously been used successfully to investigate the origin of the European populations of this pest, which all appear to come from a limited geographic region on the north shore of the Titicaca lake in Peru (Plantard et al., 2008). Microsatellite analyses were also used to reveal the phylogeographic history and reduction of allelic richness of G. pallida populations from south to north of Peru (Picard et al., 2007). ...
... Researchers are using old herbarium specimens to elucidate when and where the critical change happened that converted a blight on native plants in Mexico into a worldwide plague (Martin et al., 2013;Yoshida et al., 2013): it was contingencies among land use in Mexico, commercial ties to and livelihoods in agricultural landscapes in Europe, and the genetic architecture of Phytophthora that produced this phenomenon. Nematodes that parasitize potatoes also show both ancient phylogeographical and humancaused distribution patterns (Picard et al., 2007). There are ongoing hybridization and human-caused dispersal processes that will continue to produce risks with other taxa and in Young other places (Cooke et al., 2012;Fry and Goodwin, 1997;Goss et al., 2011). ...
The past and present impacts of humans on the biosphere have altered many ecological and evolutionary processes. One of the most dramatic set of examples comes from domestication, which has transformed species, landscapes, and socioeconomic systems over the last 30 millennia. Recent research driven by advances in molecular biology and information sciences, and enriched by whole genome analyses of the main plant and animal domesticates, is now able to elucidate obscure phylogenetic relationships complicated by past hybridization and chromosome rearrangements. These methods also reveal information on the historical events that converted wild species into useful, and in some cases, codependent taxa. A further set of human-domesticate interactions produces the great diversification behind the origin and maintenance of numerous crop landraces, fruit and vegetable variants, and animal breeds. Fashion, taste preferences, and familial dynamics are some of the additional factors involved beyond usefulness that collectively result in human-caused artificial selection. Domestication is an important dimension to consider in understanding the biogeographical implications of the Anthropocene.
... In recent years, mitochondrial genes have been used as markers to study intraspecific variation (Madani et al., 2010) and the genetic relationships among Peruvian and Canadian populations of Globodera pallida in order to identify the origin of new populations (Picard et al., 2007;Plantard et al., 2008;Madani et al., 2010). For example, mtDNA cytochrome b (cytb) gene sequences allowed the determination of the origin of new G. pallida populations (Plantard et al., 2008), which makes this a possible marker to be tested in the study of B. xylophilus intraspecific variability. ...
The pine wood nematode (PWN), Bursaphelenchus xylophilus, the causal agent of pine wilt disease (PWD), is a major world-wide pathogen and pest of pine, with impacts on forest health, natural ecosystem stability and international trade. In Portugal, PWN was first diagnosed in 1999, the first occurrence also for Europe. The disease was recently detected on the island of Madeira and in northern Spain. In an attempt to search for more reliable and robust molecular markers that enable the study of intraspecific variability of B. xylophilus from different geographic locations, the intergenic spacer (IGS) region of the 5S rRNA gene and inter-simple sequence repeats (ISSR) analysis were used to determine the genetic relationships among 43 B. xylophilus isolates from Portugal, China, Japan, South Korea and USA. IGS sequence analysis showed that this region can only be used to establish interspecific relationships, since no differences were detected among Portuguese isolates from different geographic locations. Fingerprints obtained with ISSR show high genetic variability among Portuguese isolates, except for the ones obtained prior to 2008. The ISSR dendrogram suggests the spread of the disease inside continental Portugal and to Madeira. Until 2008, B. xylophilus populations found in continental Portugal showed low genetic diversity, pointing to a single introduction, probably from Asia, whereas recent populations from continental Portugal (2009-2010) and Madeira show high genetic diversity, suggesting multiple introductions from different origins.
... Blouin (2002) showed faster substitution accumulation of mutation in nematode mtDNA than in ITS sequences and also differences in mutation rates within mitochondrial genes. However, the advantages of mtDNA exceed their limitations and it is used for species barcoding, phylogeny and phylogeographic studies in a limited number of species (Picard et al., 2007;Gutiérrez-Gutiérrez et al., 2011;Subbotin et al., 2011), mainly because of the high copy number and welldesigned COI for some groups of nematodes. Other markers used should include highly conserved genes with only one copy in the genome in order to design primers for their amplification. ...
This paper summarises the current knowledge concerning cryptic species of plant-parasitic nematode and briefly reviews the different methods available for their detection and characterisation. Cryptic species represent an important component of biodiversity, such speciation being common among plant-parasitic nematodes and occurring in diverse groups with different life history traits, including the spiral, virus vector, root-lesion and false root-knot nematodes. Cryptic species are important for a number
of reasons, including food security, quarantine, non-chemical management technologies and species conservation, and should not be ignored. The magnitude of the phenomenon is largely unknown, but the available data on plant-parasitic nematodes demonstrate that reliance on morphology alone for species delimitation seriously underestimates the total number of taxa. Future research should focus on appropriately designed case studies using combined approaches, including large-scale, whole sample analyses by next-generation sequencing or proteomics in order to be able to answer the many questions that still remain.
... Researchers are using old herbarium specimens to elucidate when and where the critical change happened that converted a blight on native plants in Mexico into a worldwide plague (Martin et al., 2013;Yoshida et al., 2013): it was contingencies among land use in Mexico, commercial ties to and livelihoods in agricultural landscapes in Europe, and the genetic architecture of Phytophthora that produced this phenomenon. Nematodes that parasitize potatoes also show both ancient phylogeographical and humancaused distribution patterns (Picard et al., 2007). There are ongoing hybridization and human-caused dispersal processes that will continue to produce risks with other taxa and in Young other places (Cooke et al., 2012;Fry and Goodwin, 1997;Goss et al., 2011). ...
Humans have altered the land cover and biogeochemical cycles of Earth, with many implications for how the study of the distributions of organisms should change. A new biogeography of the Anthropocene could help to develop additional criteria to evaluate the degree and timing of human impacts, and innovative ways to proactively manage biological diversity. Many recent studies have used paleoecological methods to evaluate no-analog conditions in the past, or modeling to evaluate possible futures. Additional approaches are needed for assessment and prediction of how new groupings of species will function ecologically under future climatic and landscape conditions, including methods for studying the effects of biotic homogenization, species extinctions, introduced species, and altered ecosystem processes.
... 10-4 Ma), and continued throughout the Pliocene in eastern Colombia (Gregory-Wodzicki, 2000;Hoorn et al., 2010;Mora et al., 2010). Some studies have revealed divergence events seemingly related to Andean uplift (Cadena et al., 2007;S€ arkinen et al., 2007;Antonelli et al., 2009;Guarnizo et al., 2009;Quintero et al., 2013), while others show that differentiation closely followed Andean orogeny (Picard et al., 2007;Ribas et al., 2007;Chaves et al., 2011). Data for Neotropical montane birds suggest a wide span of population divergence dates; some divergence events might be related to pre-Pleistocene processes and others to Pleistocene dynamics (Weir, 2009). ...
AimTo examine the effect of geographical barriers and habitat dynamics related to climatic oscillations on the phylogeography of a widespread passerine of Neotropical cloud forests, the spotted barbtail (Premnoplex brunnescens).LocationNeotropical humid forests of montane areas in lower Central America and South America.Methods
We sequenced two mitochondrial genes and one nuclear intron from specimens collected across the distribution of P. brunnescens. Phylogenetic relationships were inferred using Bayesian and maximum-likelihood methods. Groups with maximum differentiation were estimated with spatial analysis of molecular variance (SAMOVA). We estimated timing of differentiation and relationships among groups with a species-tree approach and historical demography with extended Bayesian skyline plots.ResultsSix highly differentiated clades of P. brunnescens are distributed in lower Central America, Sierra Nevada de Santa Marta, northern Venezuelan mountains, the Northern Andes, central Peru, and southern Peru and Bolivia. Within the Northern Andes clade, six phylogroups were identified associated with different slopes and isolated cordilleras. Most clades occupy opposite sides of low-lying valleys and ridgelines, but little differentiation was observed across several putative barriers. Population divergence occurred in the late Miocene and Pliocene, perhaps in association with Andean uplift. Historical fluctuations in population sizes suggest that populations tracked the spatial dynamics of montane forests associated with glacial cycles.Main conclusionsExtensive genetic differentiation in mitochondrial and nuclear DNA exists among populations of P. brunnescens. Such marked divergence was probably promoted by the rugged topography and dynamic ecological history of the Neotropical mountains. Our study sheds light on mechanisms promoting population differentiation in the montane Neotropics.
... A synopsis of landscape evolution and biotic development is provided at the end of this chapter. Local base-level changes driven by eustasy Chapter 11, and references therein turned out to coincide with estimates of critical elevations of Andean mountains (Picard et al. 2007). The Late Miocene diversifi cation of the montane genus Hedyosmum also coincided with major Andean uplift (Antonelli 2008). ...
In northern South America the Cenozoic was a period of intense tectonic and climatic interaction that resulted in a dynamic Amazonian landscape dominated by lowlands with local and shield-derived rivers. These drainage systems constantly changed shape and size. During the entire Cenozoic, the Brazilian and Guiana Shields were stable mountainous areas. Andean-derived river systems increased in importance especially in the Neogene. A remarkable feature in western Amazonian history is the waxing and waning of large lake systems and embayments. By the Late Miocene (about 11 Ma), the Andes were connected with the Atlantic through an incipient Amazon River, and from c. 7 Ma Andean-derived river systems became fully established in central and eastern Amazonia and the modern landscape configuration had developed. Rainforests already existed in northern South America during the Paleogene, but the modern rainforests – with resemblance to the Present forest – only developed during the Miocene. The western Amazonian Miocene record contains very diverse aquatic faunas (molluscs, ostracods, turtles, crocodiles, fishes) as well as terrestrial mammals. Remarkable gigantic forms thrived in Amazonian ecosystems at the time. Since the Late Miocene, edaphically heterogeneous lands emerged in western Amazonia in areas previously occupied by lake systems. At the same time nutrient-rich deposits spread over central and eastern Amazonia, an event that, based on molecular phylogenetic studies on extant taxa, coincided with diversification of terrestrial taxa. Molecular-based time estimates confirm the steady diversification and mostly pre-Quaternary origin of extant Amazonian taxa. A significant portion of the current species richness is attributed to a combination of relatively constant wet and warm climates and a heterogeneous edaphic substrate. The Quaternary was a time of distribution shifts, but can no longer be considered a time of diversification in Amazonia.
... In the cyst nematode Globodera pallida, microsatellites have previously been used successfully to investigate the origin of the European populations of this pest, which all appear to come from a limited geographic region on the north shore of the Titicaca lake in Peru (Plantard et al., 2008). Microsatellite analyses were also used to reveal the phylogeographic history and reduction of allelic richness of G. pallida populations from south to north of Peru (Picard et al., 2007). ...
The golden cyst nematode (Globodera rostochiensis), native to South America, has been introduced in many parts of the world, including Europe and North America. Recently, it was found for the first time in the province of Quebec, Canada in the locality of St. Amable near Montreal. To date, very few studies have examined the population genetics of this pest. Consequently, there is a lack of knowledge about the genetic structure and evolution of this nematode. In this study, twelve new microsatellite markers were developed in order to explore these questions. These markers were used to genotype fifteen populations originating from different regions of the world, including five from Canada. Within populations, the highest genetic diversity was consistently observed in the populations from Bolivia, the postulated region of origin of the golden nematode, and the lowest in populations from British Columbia (Canada) and New York (USA). The two Quebec populations were very similar to each other and to the population found in Newfoundland, but surprisingly, they were significantly different from three other North American populations including those from New York and British Columbia. Based on our results, we conclude that the golden cyst nematode has been introduced in North America at least twice from distinct regions of the world.
... The >99% similarity of G. ellingtonae n. sp. to G. tabacum sequences is consistent with this conclusion, and furthers the presumption that this marker also lacks sufficient variability to be useful as a molecular diagnostic for distinguishing G. pallida, G. rostochiensis, and G. tabacum. The possible existence of an additional species of PCN, particularly one originating from South America, has been the subject of study and speculation for some time (Phillips and Trudgill, 1998;Blok et al., 1998;Subbotin et al., 2000;Rumpenhorst and Ayub, 2001;Picard et al., 2007;Plantard et al., 2008;Pylypenko et al., 2008). Based on phylogenetic analysis of ITS rRNA and mitochondrial cytochrome b (cytb) sequences, Subbotin and colleagues (Madani et al., 2010;Subbotin et al., 2011) have proposed possible candidates from among South American populations of G. pallida or undescribed species, appearing in ITS rRNA trees within subclades 3, 5, and 6 (see also Table 4, this study). ...
A new species of cyst nematode, Globodera ellingtonae, is described from soil collected from a field in Oregon. Second-stage juveniles (J2) of the species are characterized by body length of 365-515 μm, stylet length of 19-22.5 μm, basal knobs rounded posteriorly and pointed anteriorly, tail 39-55 μm, hyaline tail terminus 20-32.5 μm, and tail tapering uniformly but abruptly narrowing and constricted near the posterior third of the hyaline portion, ending with a peg-like, finely rounded to pointed terminus. Cysts are spherical to sub-spherical, dark to light brown and circumfenestrate and cyst wall pattern is ridge-like with heavy punctations. Males have a stylet length of 21-25 μm and spicule length of 30-37 μm with a pointed thorn-like tip. Females have a stylet length of 20-22.5 μm, one head annule and labial disc, heavy punctations on the cuticle, and short vulval slit 7.5-8 μm long. Morphologically this new, round-cyst species differs from the related species G. pallida, G. rostochiensis, G. tabacum complex and G. mexicana by its distinctive J2 tail, and by one or another of the following: shorter mean stylet length in J2, females and males; number of refractive bodies in the hyaline tail terminus of J2; cyst morphology including Granek's ratio; number of cuticular ridges between the anus and vulva; and in the shape and length of spicules in males. Its relationship to these closely related species are discussed. Based upon analysis of ribosomal internal transcribed spacer (ITS) sequences, G. ellingtonae n. sp. is distinct from G. pallida, G. rostochiensis, G. tabacum and G. mexicana. Bayesian and Maximum Parsimony analysis of cloned ITS rRNA gene sequences indicated three clades, with intraspecific variability as high as 2.8%. In silico analysis revealed ITS restriction fragment length polymorphisms for enzymes Bsh 1236I, Hinf I, and Rsa I that overlap patterns for other Globodera species.
Due to the highly conserved structure, animal mitochondrial genome (mtDNA) is widely used in classification, evolution, phylogeny, population genetic structure and other fields. We reported on the five circle multipartite mtDNAs of a newly described species of Globodera, Globodera vulgaris (Gv) from potatoes in China. The results showed that the mtDNA of Gv was obtained through second- and third-generation sequencing, with a total length of 42,995 bp. It contained 12 protein-coding genes, two rRNA genes and 17 tRNA genes, which were distributed in different subgenomic circles. Comparison of the differences in mtDNA among Gv, G. rostochiensis, G. pallida and G. ellingtonae showed that the size and arrangement of the genes in the mtDNA of the genus Globodera were variable and not conserved. The codon usage bias of the mitochondrial protein-coding gene of Gv showed that Gv might have originated from locally and more primitive group of existing Globodera. Based on the cytochrome c oxidase subunits I genes (COX1) and the nicotinamide adenine dinucleotide dehydrogenase subunits I genes (ND1), and the results showed that Gv was clustered with Globodera spp. according to the COX1 and ND1 in scmtDNA-V, while Gv was clustered with Meloidogyne spp. according to ND1 in scmtDNA-III. The results of this study provided a new basis for understanding the multipartite structure of mtDNA as a phylogenetic and taxonomic feature of the genus Globodera. The number of subgenomic circles is a diagnostic feature of species and the arrangement order and size of mitochondrial protein-coding genes also have important application value in species identification within the genus.
Nematodes, commonly called roundworms, represent one of the largest phyla of animals. Plant- parasitic nematodes cause significant economic losses in major crops worldwide, and cyst nematodes (Heterodera spp. and Globodera spp.) are among the most damaging species. This review focuses on three main species, Globodera pallida, Globodera rostochiensis and Globodera ellingtonae, collectively known as potato cyst nematodes (PCNs). G. rostochiensis and G. pallida are the most commonly occurring species in potato- growing areas and are considered to have originated from the Andes region in South America and introduced then to Europe in the 1850s and now occur globally in more than 75 countries. PCNs feed entirely inside the root and produce distinctive cysts containing eggs. PCNs reduce root development, stunt the growth of potato plants and ultimately lead to the production of fewer and smaller tubers. PCNs are feared because of their ability to survive for up to 40 years in the soil in the absence of potatoes, and once established they are incredibly difficult to eradicate. Five case studies in this review provide an historical overview of how scientists and potato experts have responded to PCN pandemics and the effectiveness of manage-ment strategies.
This is a compilation of articles published in the Special Issue Systematics, Morphological, and Molecular Characterization of Economically Important Plant–Parasitic Nematodes: A Themed Issue in Honor of Dr. Gary Bauchan in Plants. It includes a series of original research (seven) and review articles (four) focused on plant-parasitic nematodes including two new species description, Pratylenchus dakotaensis n.sp. and Xiphinema malaka n. sp. Nematodes are one of the most
important pests globally and can cause up to 14% loss of food crops. In total, nematodes cause over $100 billion in global crop damage annually. To date, only a few thousand PPN species have been described. Nematode identification has traditionally relied on morphological and anatomical characters using light microscopy and, in some cases, scanning electron microscopy (SCN). Lately, integrative studies combining molecular diagnosis with morphology and taxonomy are used to
accurately identify and describe nematode species. Detailed analyses of morphological and molecular data have both significantly contributed to our overall understanding of the dynamic and complex nature of plant–nematode interactions. We are grateful to all the authors who submitted their work to be included in this special issue.
This datasheet on Globodera pallida covers Identity, Overview, Distribution, Dispersal, Hosts/Species Affected, Diagnosis, Biology & Ecology, Environmental Requirements, Natural Enemies, Impacts, Uses, Prevention/Control, Further Information.
This datasheet on Globodera rostochiensis covers Identity, Overview, Distribution, Dispersal, Hosts/Species Affected, Diagnosis, Biology & Ecology, Environmental Requirements, Natural Enemies, Impacts, Uses, Prevention/Control, Further Information.
Cyst nematodes are sedentary endoparasites of plants which cause important economic losses worldwide. New nematode control measures are needed since the removal of effective chemical nematicides from the market due to their negative impact on environment and human health. Induced hatching of second-stage juveniles in the absence of host plant using root exudates, also named “suicide hatching”, could be a sustainable alternative method to reduce nematode population densities in infested soils. Unfortunately, biocontrol methods are often less effective in agricultural fields than in laboratory or greenhouse and this could be due to, among other reasons, a different susceptibility of nematode populations to root exudate stimulation. Testing this intra-specific variability would help to anticipate any drop in the efficiency of this new biocontrol strategy. A selection of root exudates from different plant species, maximizing the hatching level highlighted in a previous study, was tested on the hatching of representative populations of the genetic diversity for Globodera pallida, Heterodera schachtii and Heterodera carotae. Results showed significant differences between populations for given nematode species but not correlated with the genetic structure. Overall, root exudates tested provide a high level of hatching of these three nematode species. Surprisingly, the root exudate from broccoli induces hatching of European populations of the potato cyst nematode G. pallida. © 2021, Koninklijke Nederlandse Planteziektenkundige Vereniging.
Since the first detection of Globodera pallida in Costa Rica in 2005, no further research has been done to study the presence and distribution of potato cyst nematodes in the country. The objectives of this study were to identify with molecular approaches the Globodera species and their distribution in Cartago, Costa Rica, and to determine the nematode intraspecific variability. Fourteen populations were collected at three elevations in the north of Cartago. In addition, one Globodera population collected from Alajuela (the second largest potato area in the country) was included in the molecular analysis. Fifteen populations were characterized with a segment of the ribosomal DNA, ITS1-5.8S-ITS2 (ITS), and the partial mitochondrial DNA gene, cytochrome b (cytb). A unique G. pallida haplotype from each marker was identified from 202 cytb sequences and 188 ITS sequences, suggesting a single introduction into the country and then spread. The phylogenetic relationships based on the cytb marker showed that the G. pallida populations from Costa Rica have a unique origin, possibly from the northern region of Peru. A pathotype identification study is suggested for the development of nematode-resistant potato varieties in Costa Rica. RESUMEN Sandoval-Ruiz, R., L. Flores-Chaves, and D. A. Humphreys-Pereira. 2020. Caracterización molecular y distribución de Globodera pallida en la principal área productora de papa de Costa Rica. Nematropica 50:218-228. Desde la primera detección de Globodera pallida en Costa Rica en el 2005, no se han realizado investigaciones para estudiar la presencia y distribución de nematodos del quiste de la papa en el país. Los objetivos de este estudio fueron identificar mediante técnicas moleculares las especies de Globodera y su distribución en Cartago, y determinar la variabilidad intraespecífica. Catorce poblaciones fueron muestreadas en tres estratos altitudinales en el norte de Cartago. Adicionalmente, una población de Globodera colectada en Alajuela (la segunda principal área productora de papa en el país) fue incluida en el análisis molecular. Las 15 poblaciones se caracterizaron con un segmento del ADN ribosomal, ITS1-5.8S-ITS2 (ITS) y el gen parcial de ADN mitocondrial, citocromo b (cytb). Un único haplotipo de cada Molecular characterization of Globodera pallida in Costa Rica: Sandoval-Ruiz et al. 219 marcador fue identificado de 202 secuencias del cytb y 188 secuencias del ITS, lo que sugiere un único sitio de entrada y de ahí se distribuyó al resto del área. Las relaciones filogenéticas basadas en el marcador cytb mostraron que las poblaciones de G. pallida de Costa Rica poseen un único origen, y posiblemente de la región norte de Perú. Se sugiere un estudio de identificación de patotipos para el desarrollo de variedades de papa resistentes al nematodo en el país.
Mitogenomic diversity and genetic population structure of the pinewood nematode (PWN) Bursaphelenchus xylophilus inhabiting Kyushu, Japan were analyzed. A method for performing long PCR using single nematodes and sequencing nematode mitochondrial genomes individually is presented here. About 8 kb (∼55%) of the complete mitochondrial genome was successfully obtained from 285 individuals collected from 12 populations. The 158 single nucleotide polymorphisms detected corresponded to 30 haplotypes, clearly classified into two clades. Haplotype diversity was 0.83, evidencing a remarkable high diversity within Kyushu. The high genetic differentiation among the 12 populations (0.331) might be due to past invasion and expansion routes of PWN in northeastern and southeastern Kyushu. The distinct genetic composition of populations within the northwestern, central western, and southwestern Kyushu seems to be mostly related to the extinction of pine forests and long-range migration of PWN due to human activity. Overall, direct long PCR and sequencing of single nematode individuals are effective methods for investigating mitochondrial polymorphisms, and these are effective tools for PWN population genetics and other intraspecific studies.
L’étude des modifications phénotypiques et génomiques associées à l’adaptation des pathogènes aux résistances est une étape fondamentale pour mieux comprendre et anticiper le phénomène de contournement des résistances. Le nématode à kyste Globodera pallida est un important pathogène de la pomme de terre, vis-à-vis duquel un QTL majeur de résistance, GpaVvrn, a été identifié chez Solanum vernei. Cependant, la capacité des populations de G. pallida à s’adapter à cette résistance en quelques générations seulement a été mise en évidence par évolution expérimentale. Dans ce contexte, ce travail de thèse avait pour objectifs (1) d’étudier les traits d’histoire de vie du nématode impactés par l’adaptation, afin de tester l’existence éventuelle d’un coût de virulence, et (2) d’identifier les régions génomiques impliquées dans l’adaptation, par une approche originale combinant évolution expérimentale et scans génomiques sur des lignées virulentes et avirulentes. Contre toute attente, nous avons montré que l’adaptation à la résistance issue de S. vernei entraînait une augmentation de la fitness des individus virulents sur hôte sensible. Nous avons également pu identifier des régions génomiques candidates à l’adaptation à la résistance de la plante hôte, contenant des gènes codant pour des effecteurs, et notamment des SPRYSECs, connus chez les nématodes à kyste pour être impliqués dans la suppression des défenses des plantes mais aussi dans la virulence du nématode. À terme, ces résultats s’avéreront utiles pour la conception de stratégies durables de déploiement de variétés de pommes de terre résistantes.
Correct identification of species and pathotypes is must for eradication of potato cyst nematodes (PCN). The identification of PCN species after completing the life cycle is very difficult because it is based on morphological and morphometrical characteristics. Genetically different populations of PCN are morphologically same and differentiated based on the host differential study. Later on these traditional techniques have been replaced by biochemical techniques viz, one and two dimensional gel electrophoresis, capillary gel electrophoresis, isozymes, dot blot hybridization and isoelectric focusing etc. to distinguish both the species. One and two dimensional gel electrophoresis has used to examine inter- and intra-specific differences in proteins of Globodera rostochiensis and G. pallida. Now application of PCR and DNA based characterization techniques like RAPD, AFLP and RFLP are the important tools for differentiating inter- and intra specific variation in PCN and has given opportunities to accurate identification of PCN. For managing the PCN, till now we are following integrated pest management (IPM) strategies, however these strategies are not effective to eradicate the PCN. Therefore to eradicate the PCN we need noval management practices like RNAi (RNA interference) or Gene silencing.
The fish faunas of continental South and Central America constitute one of the greatest concentrations of aquatic diversity on Earth, consisting of about 10 percent of all living vertebrate species. Historical Biogeography of Neotropical Freshwater Fishes explores the evolutionary origins of this unique ecosystem. The chapters address central themes in the study of tropical biodiversity: why is the Amazon basin home to so many distinct evolutionary lineages? What roles do ecological specialization, speciation, and extinction play in the formation of regional assemblages? How do dispersal barriers contribute to isolation and diversification? Focusing on whole faunas rather than individual taxonomic groups, this volume shows that the area's high regional diversity is not the result of recent diversification in lowland tropical rainforests. Rather, it is the product of species accumulating over tens of millions of years and across a continental arena.
The health and economic importance of parasitic nematodes cannot be overstated. Moreover, they offer a complex and diverse array of life strategies, raising a multitude of evolutionary questions. Researchers are applying population genetics to parasitic nematodes in order to disentangle some aspects of their life strategies, improve our knowledge about disease epidemiology, and design control strategies. However, population genetics studies of nematodes have been constrained due to the difficulty in sampling nematodes and developing molecular markers. In this context, new computational and sequencing technologies represent promising tools to investigate population genomics of parasitic, non-model, nematode species in an epidemiological context.
In the quantitative phyletic approach to evolutionary taxonomy, quantitative methods are used for inferring evolutionary relationships. The methods are chosen both for their operationism and for their connection to evolutionary theory and the goals of evolutionary taxonomy. As an example of this approach, a detailed analysis of a set of anuran characters is presented and taxonomic conclusions based on those characters are drawn. The methods and conclusions of the quantitative phyletic analysis are compared and contrasted with the methods of previous workers in the field of anuran classification.
Solanum sect. Petota series Conicibaccata is a group of 40 wild potato species, composed of diploids, tetraploids, and hexaploids, distributed from central Mexico to central Bolivia. This study examined their species boundaries and interrelationships by phenetic analyses of morphological data and cladistic analyses of chloroplast DNA restriction site data. Mitotic chromosome counts were obtained for 114 accessions; species whose first counts are reported here are S. garcia-barrigae, S. orocense, and S. sucubuncnse. Most results were concordant in showing three main groups of species: 1) tetraploids and hexaploids from central Mexico to southern Ecuador; 2) diploids from northern Peru to Bolivia, included in a cpDNA clade of diploids and hexaploids assigned to ser. Demissa and ser. Tuberosa, and 3) diploids and tetraploids from southern Colombia to Peru, cladistically related to members of ser. Piuranu. Some species boundaries, and even series boundaries of ser. Conicibaccata and ser. Piurana, are supported morphologically only by a combination of widely overlapping character states, none of which is constant for a species. Other species have no support, and it is likely that too many species are recognized in the group. The cladistic analysis of chloroplast DNA data suggested that some species represent a combination of apospecies and plesiospecies, and some populations are of possible hybrid origin.
Genetic diversity at nine isozyme loci was surveyed in an endangered tree species, the argan tree, endemic to south-western Morocco. The species is highly diverse (3.6 alleles/locus) with populations strongly differentiated from each other (F ST=0.25). This example is used to illustrate a method for standardizing measures of allelic richness in samples of unequal sample sizes, which was developed for the estimation of the number of species and relies on the technique of rarefaction. In addition, it is shown that the measure of subdivision, θ ST, obtained when allelic richness is used in place ofh (Nei's index of diversity), is much larger than the F ST [e.g. θ ST(40)=0.52, where (40) indicates the specified sample used to estimate the allelic richness]. This suggests that rare alleles (which strongly influence measures of allelic richness) have a more scattered distribution than more frequent ones, a result which raises special conservation issues for the argan tree.
Sedimentological data indicate that a semi-arid/arid climate prevailed across the Central Andes from 15 Ma to 4 Ma. Between 4 and 3 Ma a switch to hyperaridity occurred along the western margin of South America. Palaeoaltitude data suggest that a substantial proto-Central Andean mountain range was in place between 15 and 9 Ma. These data support the idea that the Andean rain shadow existed by 15 Ma and that it reinforced the preexisting climatic regime rather than changing it. The change to hyperaridity in western South America is attributed to a combination of global climate cooling and enhanced upwelling of the Humboldt current generated by closure of the Central American Seaway between 3.5 and 3 Ma, and not to the Andean rain shadow.
The Nuffield Council on Bioethics1,2 suggests that introgression of genetic material into related species in centres of crop bio-diversity is an insufficient justification to bar the use of genetically modified crops in the developing world. They consider that a precautionary approach to forgo the possible benefits invokes the fallacy of thinking that doing nothing is itself without risk to the poor. Here we report findings relevant to this and other aspects of environmental biosafety for genetically modified potato in its main centre of biodiversity, the central Andes. We studied genetically modified potato clones that provide resistance to nematodes, principal pests of Andean potato crops. We show that there is no harm to many non-target organisms, but gene flow occurs to wild relatives growing near potato crops. If stable introgression were to result, the fitness of these wild species could be altered. We therefore transformed the male sterile cultivar Revolucion to provide a genetically modified nematode-resistant potato to evaluate the benefits that this provides until the possibility of stable introgression to wild relatives is determined. Thus, scientific progress is possible without compromise to the precautionary principle.
TheOxalis tuberosa alliance is a group of morphologically similarOxalis species allied to the Andean tuber crop oca,O. tuberosa. Originally described by cytologists as a dozen species sharing a base chromosome number rare inOxalis (x = 8), the alliance as defined here includes additional species for which cytological information is not yet available but which are supported as members on molecular and/or morphological grounds. The alliance includes members found in the Andean region from Venezuela to northern Argentina, with one species at high elevations in Central America. They occur from the high Andean steppes (páramo and puna) to the cloud forests of middle elevations and include both restricted endemics and variable widespread species complexes.
Geographical and altitudinal distributions of members of the alliance and selectedOxalis species outside the alliance were compared with a combined phylogenetic analysis of DNA sequence data of ITS and ncpGS (chloroplast-expressed glutamine synthetase). Groups within the alliance (i.e., major clades on the molecular trees) occur across widespread, overlapping regions in the Andes, with only partial ecological separation. The hypothesis that theO. tuberosa alliance may have developed in the Andes of southern Peru and northwestern Bolivia and radiated southward and, especially, northward along the Andean axis is suggested by patterns of distributions of members of the alliance and outgroups. In spite of uncertain species delimitations, it is clear that the alliance includes many endemic species and ecotypes that have very restricted distributions. As relatives of the Andean tuber cropOxalis tuberosa, the genetic diversity represented by this geographical variability should be a high priority for conservation.
The Commonwealth Potato Collection contains 77 species following the incorporation of the personal collection of Professor
JG Hawkes. The material originates from several expeditions to the Americas and represents a potentially valuable source of
resistance to pests and pathogens, including potato cyst nematodes (PCN). The germplasm from the Hawkes collection screened
in this study included taxa mainly from Mexico, Bolivia, Argentina and Peru. Seedlings of 198 accessions, from 63 different
species were screened for reaction to the PCN species G. pallida and G. rostochiensis. Of the 198 accessions tested, 56% contained G. pallida-resistant clones and 53% contained clones resistant to G. rostochiensis. Twelve species in this survey are believed to contain novel, previously unreported sources of resistance. The geographical
distribution of resistance indicated a
contrast between the two PCN species. Although, as in previous studies, resistance to G. rostochiensis was centred on Bolivia and Argentina, G. pallida resistance was found across the geographical range of tuber-bearing Solanum. The possibility of cross-resistance arising from selective pressure from the more northern species G. mexicana is discussed.
A maximum likelihood method for inferring evolutionary trees from DNA sequence data was developed by Felsenstein (1981). In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly.The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.
The accuracies and efficiencies of four different methods for constructing phylogenetic trees from molecular data were examined by using computer simulation. The methods examined are UPGMA, Fitch and Margoliash's (1967) (F/M) method, Farris' (1972) method, and the modified Farris method (Tateno, Nei, and Tajima, this paper). In the computer simulation, eight OTUs (32 OTUs in one case) were assumed to evolve according to a given model tree, and the evolutionary change of a sequence of 300 nucleotides was followed. The nucleotide substitution in this sequence was assumed to occur following the Poisson distribution, negative binomial distribution or a model of temporally varying rate. Estimates of nucleotide substitutions (genetic distances) were then computed for all pairs of the nucleotide sequences that were generated at the end of the evolution considered, and from these estimates a phylogenetic tree was reconstructed and compared with the true model tree. The results of this comparison indicate that when the coefficient of variation of branch length is large the Farris and modified Farris methods tend to be better than UPGMA and the F/M method for obtaining a good topology. For estimating the number of nucleotide substitutions for each branch of the tree, however, the modified Farris method shows a better performance than the Farris method. When the coefficient of variation of branch length is small, however, UPGMA shows the best performance among the four methods examined. Nevertheless, any tree-making method is likely to make errors in obtaining the correct topology with a high probability, unless all branch lengths of the true tree are sufficiently long. It is also shown that the agreement between patristic and observed genetic distances is not a good indicator of the goodness of the tree obtained.
The geographic distribution of wild potatoes (Solanaceae sect. Petota) was analyzed using a database of 6073 georeferenced observations. Wild potatoes occur in 16 countries, but 88% of the observations are from Argentina, Bolivia, Mexico, and Peru. Most species are rare and narrowly endemic: for 77 species the largest distance between two observations of the same species is <100 km. Peru has the highest number of species (93), followed by Bolivia (39). A grid of 50 × 50 km cells and a circular neighborhood with a radius of 50 km to assign points to grid cells was used to map species richness. High species richness occurs in northern Argentina, central Bolivia, central Ecuador, central Mexico, and south and north-central Peru. The highest number of species in a grid cell (22) occurs in southern Peru. To include all species at least once, 59 grid cells need to be selected (out of 1317 cells with observations). Wild potatoes occur between 38° N and 41° S, with more species in the southern hemisphere. Species richness is highest between 8° and 20° S and around 20° N. Wild potatoes typically occur between 2000 and 4000 m altitude.
Recent advances in biochrology, geochrology, magnetostratigraphy, structural geology, and basin analysis make untenable the traditional correlation of the first major Andean-age deformational episode in Bolivia with the middle Eocene "Incaic tectonic phase" defined in central Peru and intead demostrate that the episode took place in late Oligocene and early Miocene time. This major tectonic crisis resulted in contemporary development of the Subandean external foreland basin and Altiplano intermontana basin, which were separeted by the initiation of thrusting in the present Cordillera Oriental area. The deformation suggests that the Bolivian orocline began to develop at that time. It is likely that this tectonic upheaval is genetically linked to the maked increase in rate of plate convergence produced by the contemporaneus creakup of the Farallon plate. (Résumé d'auteur).
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
The juveniles of Globodera "mexicana" invade the roots of potato and tomato, but only in the latter they initiate syncytia and develop into adult males and females. In vitro hybridisations were conducted between five populations of G. "mexicana" and two of G. pallida. Back-crosses were also made using females of G. pallida. The behaviour of the hybrids was studied on potato and tomato cultivated in Petri dishes. The F1s were able to induce syncytia in both plants. Depending of the G. pallida population used, these syncytia allowed the nematodes to develop into both male and female or only into male. In the latter case, the ability to develop into female increased with the number of back-crosses. The degree of cytoplasmic incompatibility depends of the parents used. With the Duddingston population of G. pallida Pa1, the incompatibility was weak. These results are used to discuss the concept of species and speciation.
New fossil murids discovered in South Asian and African localities dated from 15 to 12 m.y. ago define the age interval of 12 to 8 m.y. for the Mus-Rattus divergence time. Discrepancy with the molecular data must therefore be explained by higher rates of amino-acid substitutions in some proteins and of genomic evolution as suggested by recent works. Within rodents, the murids seem to show high rates of molecular evolution. -Authors
The genes encoding body-wall-specific glyceraldehyde-3-phosphate dehydrogenase from Caenorhabditis briggsae were sequenced and compared to the homologous genes from Caenorhabditis elegans. The direct tandem organization of these genes, gpd-2 and gpd-3, and the size and location of the two introns in each gene are the same in C elegans and C. briggsae. Primer-extension studies demonstrated that the two genes in C. briggsae are trans-spliced differentially with the same splice leader (SL) RNAs as are observed in C. elegans. The gpd-2 gene is trans-spliced with SL1 while gpd-3 is trans-spliced with SL2. Significant sequence conservation was observed within the promoter regions of each species and may indicate those regions responsible for body-wall-muscle-specific gene expression and/or differential trans-splicing. Comparisons of the sequences suggest that the tandem repeat of the genes has been subjected to concerted evolution and that C. briggsae and C. elegans diverged much earlier than would be anticipated based on morphological similarities alone. Finally, an open reading frame found several hundred nucleotides upstream from gpd-2, in both species, appears to be homologous to the ATP synthase subunit, ATPase inhibitor protein, from bovine mitochondria.
1-Trimethylsilyl-1,3-diyne derived trans-bis(trimethylstannyl) enynes undergo stepwise transmetallation with methyllithium to furnish the corresponding enynyllithium reagents. The application, in various orders, of a sequence of transmetallation-protonation-alkylation-hydroxyalkylation-hydroboration-oxidation reactions provides a novel approach to stereo-defined β-alkylidene γ-lactones and β, γ-unsaturated δ-lactones.
We report paleomagnetic data from 73 sites (628 samples) of upper Oligocene to Pliocene rocks from central and northern Peru. The data indicate that the Subandean Zone has not experienced vertical axis rotation since the upper Oligocene, whereas the coast and the Western Cordillera record a coherent pattern of counterclockwise rotations emplaced in the last 10 Ma. This pattern can best be explained by two competing hypotheses: (1) a propagation in rotations from the Bolivian Orocline toward the north or (2) a more punctual and widespread event linked to subduction of the Nazca Ridge that caused the rotations. On the basis of the time-space relationship of paleomagnetic rotations, deformation, magmatism and Nazca-South America plate convergence, the latter appears more likely. Moreover, because the rotations north of the Abancay deflection (~15.5°S) are synchronous with deformation and exhumation, they indicate that major mountain building in the Peruvian Andes has occurred since 10 Ma. Finally, we suggest that a succession of aseismic ridge subduction events played an important role in shaping the modern topography of the Andean chain.
Seven wild diploid potato species, Series Tuberosa, representing 1023 clones were screened for resistance to the potato cyst nematode, Globodera pallida. Over 25% of the clones were resistant to pathotype P4A and almost 30% were resistant to pathotype P5A. The resistance in hybrid progenies of these and other resistant species with cultivated potatoes was evaluated, and over 2200 seedlings were screened. High frequencies of resistance (>50%) to P4A were found in progenies with Solanum leptophyes, S. vernei, S. gourlayi and S. capsicibaccatum, whereas resistance to P5A was found in these species as well as S. sparsipilum. The importance of nematode resistant wild species for potato breeding is discussed.
The elevation of the Andean Cordillera is a crucial boundary condi- tion for both climatic and tectonic studies. The Andes affect climate be- cause they form the only barrier to atmospheric circulation in the Southern Hemisphere, and they intrigue geologists because they have the highest plateau on Earth formed at a noncollisional plate margin, the Altiplano-Puna. Yet, until recently, few quantitative studies of their uplift history existed. This study presents both (1) a review of the quan- titative paleoelevation estimates that have been made for the Central and Colombian Andes and (2) an examination of the source and mag- nitude of error for each estimate. In the Central Andes, paleobotanical evidence suggests that the Altiplano-Puna had attained no more than a third of its modern elevation of 3700 m by 20 Ma and no more than half its modern elevation by 10.7 Ma. These data imply surface uplift on the order of 2300-3400 m since the late Miocene at uplift rates of 0.2-0.3 mm/yr. Paleobotanical and geomorphological data suggest a similar uplift history for the Eastern Cordillera—namely no more than half the modern elevation present by 10 Ma. No evidence exists for an exponential increase in uplift rate, as has been interpreted from fission- track data. These uplift rates mostly reflect mean surface uplift rather than rock uplift—that is, uplift of material points—because little dis- section of the western Eastern Cordillera has occurred south of lat 19°S and of the Altiplano-Puna. Thus, the Central Andean Plateau appears to be young. In the Colombian Andes, paleobotanical data imply rapid uplift of the Eastern Cordillera between 2 and 5 Ma at rates on the or- der of 0.6-3 mm/yr. However, some of this uplift is likely rock uplift due to erosion-driven isostatic rebound rather than mean surface uplift.
Fitch, W. M. (Dept. of Physiological Chemistry, Univ. of Wisconsin, Madison, Wisconsin, 53706), 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool., 20:406-416.A method is presented that is asserted to provide all hypothetical ancestral character states that are consistent with describing the descent of the present-day character states in a minimum number of changes of state using a predetermined phylogenetic relationship among the taxa represented. The character states used as examples are the four messenger RNA nucleotides encoding the amino acid sequences of proteins, but the method is general.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
The emergence of agriculture in the Near East also involved the domestication of einkorn wheat. Phylogenetic analysis that
was based on the allelic frequency at 288 amplified fragment length polymorphism molecular marker loci indicates that a wild
group of Triticum monococcum boeoticum lines from the Karacadağ mountains (southeast Turkey) is the likely progenitor of cultivated einkorn varieties. Evidence
from archeological excavations of early agricultural settlements nearby supports the conclusion that domestication of einkorn
wheat began near the Karacadağmountains.
Twenty six populations of potato cyst-nematodes from Colombia, Ecuador, Peru and Bolivia were examined and identified as Heterodera rostochiensis Woll. or H. pallida Stone. North of 15.6°S only H. pallida was found, but south of this latitude most populations examined were H. rostochiensis or a mixture of the two species. Possible reasons for the distribution of the two species being dependent on latitude are discussed, particularly the influence of daylength.
Potato cyst-nematode species are believed to have evolved in South America but now have a worldwide distribution and can be major and persistent pests except in the warmest soils. Both species contain pathotypes and their correct identification, although difficult, is important when planning control with resistant potatoes. Some closely related and very similar species are of minor economic importance. Resistant cultivars available at present are effective against only some pathotypes and except where high crop values make use of nematicides economic, it is important to combine extended crop rotation with such cultivars.
THE South American Andes were brought to their present height by the final uplift phases of the late Pliocene and the Pleistocene1–6 and an alpine-like vegetation (locally called páramo or puna7–14) developed in the terrain thus produced. It follows that the evolution of the associated páramo-puna fauna by multiple speciation in situ should have taken place mostly or entirely during the Quaternary, so that the occurrence of speciation within this fauna should be a convenient guide to the possible rate of speciation in the Pleistocene.
Cloud forests are distributed in the Neotropics, from northern Mexico to Argentina, under very specific ecological conditions, namely slopes with high humidity input from clouds and mist. Its distribution in Mesoamerica is highly fragmented, similar to an archipelago, and taxa are thus frequently represented as sets of isolated populations, each restricted to particular mountain ranges and often showing a high degree of divergence, both morphologically and genetically. The common bush-tanager (Chlorospingus ophthalmicus, Aves: Thraupidae) inhabits cloud forests from eastern and southern Mexico south to northwestern Argentina. Here we use 676bp of mtDNA (around the ATPase 8 gene) to explore the genetic variation and phylogeographic structure of the Mexican populations of C. ophthalmicus. Phylogenetic analyses of mtDNA sequences indicate deep genetic structure. Five major clades, which segregate according to geographic breaks, are identified (starting from the deepest one in the phylogeny): (1) Southern Chiapas and Northern Central America, (2) Tuxtlas massif, (3) Sierra Madre del Sur, (4) Eastern Oaxaca and Northern Chiapas, and (5) Sierra Madre Oriental. The long history of isolation undergone by each clade, as suggested by the phylogeny, implies that the species status of each of them should be revised.
We report the isolation of five microsatellites loci from the sugar beet cyst nematode (Heterodera schachtii). Multilocus genotypes were obtained on individual larvae freshly emerged from cysts. Allelic diversity ranged from four to 27 among the five loci. The primers were tested for cross-species amplification in six other species of phytoparasitic nematodes of the Heterodera genus. Those molecular markers will be used to study the genetic structure of this obligatory parasite and how it is affected by the use of resistant plants.
The Quaternary cold periods in Europe are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in both animals and plants. The phylogeographies of 10 taxa, including mammals (Ursus arctos, Sorex spp., Crocidura suaveolens, Arvicola spp.), amphibians (Triturus spp.), arthropods (Chorthippus parallelus), and plants (Abies alba, Picea abies, Fagus sylvatica, Quercus spp.), were analysed to elucidate general trends across Europe. Only a small degree of congruence was found amongst the phylogeographies of the 10 taxa, but the likely postglacial colonization routes exhibit some similarities. A Brooks parsimony analysis produced an unrooted area phylogram, showing that: (i) the northern regions were colonized generally from the Iberic and Balkanic refugia; and (ii) the Italian lineages were often isolated due to the presence of the Alpine barrier. The comparison of colonization routes highlighted four main suture-zones where lineages from the different refugia meet. Some of the intraspecific genetic distances among lineages indicated a prequaternary divergence that cannot be connected to any particular cold period, but are probably related mainly to the date of arrival of each taxon in the European continent. As a consequence, molecular genetics so far appears to be of limited use in dating Quaternary events.
Aim The lizard genus Proctoporus Tschudi, 1845 was used as a model to test the South‐to‐North Speciation Hypothesis (SNSH) for species groups occurring in the Andes Mountains of South America. This hypothesis proposes that speciation of high Andean taxa followed a south‐to‐north pattern, generally coinciding with the progression of final uplift of the Andes. According to SNSH, a phylogenetic hypothesis of relationships of a taxonomic group occurring in the high Andes would show a branching pattern in which the southernmost species diverged first, followed by the more northern species, and so on in a northerly pattern.
Location The central and northern Andes Mountains in South America.
Methods A phylogenetic hypothesis was reconstructed for all species of the lizard genus Proctoporus by examining the external morphology of 341 individuals. This phylogeny was then examined to determine monophyly of the genus, distribution patterns of species groups, and congruence with SNSH.
Results The genus Proctoporus did appear to be monophyletic and, therefore, it was valid to use this group to assess SNSH. The southernmost species were found to be the most basal, which was consistent with SNSH. The species occurring in the northern Andes did not exactly match the SNSH prediction. The Venezuelan and Trinidadian species did appear to be highly derived, as predicted by the hypothesis, but the Ecuadorian and Colombian species did not form a particular pattern in relation to the hypothesis.
Main conclusions The SNSH does appear to have predictive power with regard to large‐scale distribution patterns. The finer‐scale patterns of speciation in the Andes, however, appear to be a more complex phenomenon that cannot be fully explained by a simple hypothesis. It is important to have a testable hypothesis in hand with which to compare data from disparate species groups. The incorporation of phylogenetic data of other high Andean taxa with similar distribution patterns is necessary to determine the full utility of SNSH in explaining evolutionary patterns in the Andes of South America.
This paper reviews the systematics of wild potatoes over the past 11 years, in reference to the latest comprehensive taxonomic treatment by Hawkes (1990. The potato: evolution, biodiversity and genetic resources. Belhaven Press, Washington, D.C.). Included here is information on monographs and floras, new germplasm collections made since 1988 compared to total potato distributional data, new taxonomic changes (including synonymy and new species descriptions), ingroup and outgroup relationships, intraspecific studies, diversity studies, and fingerprinting. In addition, data supporting taxonomic changes and phylogeny from ploidy levels, Endosperm Balance Numbers, and morphological studies of taxonomically important characters are reviewed. A revised list of 206 species is presented (from 232 in Hawkes) that incorporates recent synonymy of names, recognition of new names, and new species descriptions. New germplasm collections of 58 potato taxa were collected that did not occur in genebanks before 1988.
Accessions obtained from the Commenwealth Potato Collection were evaluated for resistance to European populations of potato cyst-nematodes (PCN). With over 36% of the current collection assessed, resistance to pathotypes of both Globodera rostochiensis and G. pallida were identified in 16 species from Argentina, Bolivia or Peru. Resistance to all PCN pathotypes was particularly prevalent in species from the Andean regions of Bolivia and North Argentina, supporting the hypothesis of co-evolution of the potato and PCN in these regions.
Thomas Lynch (1971) has recently attempted to document the fact that the preceramic hunter-gatherers of Peru were mobile throughout
a range of altitudinal zones and that the fields of movement of these preceramic populations may well have been continuous,
since the members of each group exploited the resources of different habitats in terms of regular annual cycles. However,
it is equally clear that these long, linear fields of the preceramic populations began to be fragmented at some point in lime.
We believe that the termination of the proposed period of transhumance constitutes an extremely interesting problem. At the
present time this feature has been discussed only in terms of data from the Peruvian coast. In this paper we employ some of
Lynch’s data and observations in an attempt to demonstrate (I) that a minimum of modification of the preceramic pattern of
food procurement within the highlands was required to convert hunter-gatherers into food producers; and (2) wild tubers played
a crucial role in this process.
An attempt has been made to establish a procedure for estimating the course taken by evolution. The model used is that of a branching random walk, which is strictly valid only when the causes of divergence between populations are random genetic drift and variable selection. With suitable transformations of the data, evolution can then be considered as a branching Brownian-motion process. To keep the model as simple as possible it was supposed that no population becomes extinct and that each population splits, at a random time, into two daughter populations each identical to its parent. The problem was to estimate the form and dimensions of the most probable tree uniting the presently living populations. The ideal method of estimation, maximum likelihood, proved difficult and had to be replaced in part by alternative procedures. In addition to describing the available procedures in detail, a simple example is worked out fully, and the logical content and limitations of the methods are considered in depth.
The association between two or more lineages over evolutionary time is a recurrent theme spanning several different fields within biology, from molecular evolution to coevolution and biogeography. In each `historical association', one lineage is associated with another, and can be thought of as tracking the other over evolutionary time with a greater or lesser degree of fidelity. Examples include genes tracking organisms, parasites tracking hosts and organisms tracking geological and geographical changes. Parallels among these problems raise the tantalizing prospect that each is a special case of a more general problem, and that a single analytical tool can be applied to all three kinds of association.
Most of the earth's terrestrial species live in the soil. These organisms, which include many thousands of species of fungi and nematodes, shape aboveground plant and animal life as well as our climate and atmosphere. Indeed, all terrestrial ecosystems consist of interdependent aboveground and belowground compartments. Despite this, aboveground and belowground ecology have been conducted largely in isolation. This book represents the first major synthesis to focus explicitly on the connections between aboveground and belowground subsystems--and their importance for community structure and ecosystem functioning. David Wardle integrates a vast body of literature from numerous fields--including population ecology, ecosystem ecology, ecophysiology, ecological theory, soil science, and global-change biology--to explain the key conceptual issues relating to how aboveground and belowground communities affect one another and the processes that each component carries out. He then applies these concepts to a host of critical questions, including the regulation and function of biodiversity as well as the consequences of human-induced global change in the form of biological invasions, extinctions, atmospheric carbon-dioxide enrichment, nitrogen deposition, land-use change, and global warming. Through ambitious theoretical synthesis and a tremendous range of examples, Wardle shows that the key biotic drivers of community and ecosystem properties involve linkages between aboveground and belowground food webs, biotic interaction, the spatial and temporal dynamics of component organisms, and, ultimately, the ecophysiological traits of those organisms that emerge as ecological drivers. His conclusions will propel theoretical and empirical work throughout ecology.
The genes encoding body-wall-specific glyceraldehyde-3-phosphate dehydrogenase from Caenorhabditis briggsae were sequenced and compared to the homologous genes from Caenorhabditis elegans. The direct tandem organization of these genes, gpd-2 and gpd-3, and the size and location of the two introns in each gene are the same in C. elegans and C. briggsae. Primer-extension studies demonstrated that the two genes in C. briggsae are trans-splice differentially with the same splice leader (SL) RNAs as are observed in C. elegans. The gdp-2 gene is trans-spliced with SL1 while gdp-3 is trans-spliced with SL2. Significant sequence conservation was observed within the promoter regions of each species and may indicate those regions responsible for body-wall-muscle-specific gene expression and/or differential trans-splicing. Comparisons of the sequences suggest that the tandem repeat of the genes has been subjected to concerted evolution and that C. briggsae and C. elegans diverged much earlier than would be anticipated based on morphological similarities alone. Finally, an open reading frame found several hundred nucleotides upstream from gpd-2, in both species, appears to be homologous to the ATP synthase subunit, ATPase inhibitor protein, from bovine mitochondria.