Phylogenetic Relationships and Genetic Variation in Longidorus and Xiphinema Species (Nematoda: Longidoridae) Using ITS1 Sequences of Nuclear Ribosomal DNA

Genetic analyses using DNA sequences of nuclear ribosomal DNA ITS1 were conducted to determine the extent of genetic variation within and among Longidorus and Xiphinema species. DNA sequences were obtained from samples collected from Arkansas, California and Australia as well as 4 Xiphinema DNA sequences from GenBank. The sequences of the ITS1 region including the 3'' end of the 18S rDNA gene and the 5'' end of the 5.8S rDNA gene ranged from 1020 bp to 1244 bp for the 9 Longidorus species, and from 870 bp to 1354 bp for the 7 Xiphinema species. Nucleotide frequencies were: A = 25.5%, C = 21.0%, G = 26.4%, and T = 27.1%. Genetic variation between the two genera had a maximum divergence of 38.6% between X. chambersi and L. crassus. Genetic variation among Xiphinema species ranged from 3.8% between X. diversicaudatum and X. bakeri to 29.9% between X. chambersi and X. italiae. Within Longidorus, genetic variation ranged from 8.9% between L. crassus and L. grandis to 32.4% between L. fragilis and L. diadecturus. Intraspecific genetic variation in X. americanum sensu lato ranged from 0.3% to 1.9%, while genetic variation in L. diadecturus had 0.8% and L. biformis ranged from 0.6% to 10.9%. Identical sequences were obtained between the two populations of L. grandis, and between the two populations of X. bakeri. Phylogenetic analyses based on the ITS1 DNA sequence data were conducted on each genus separately using both maximum parsimony and maximum likelihood analysis. Among the Longidorus taxa, 4 subgroups are supported: L. grandis, L. crassus, and L. elongatus are in one cluster; L. biformis and L. paralongicaudatus are in a second cluster; L. fragilis and L. breviannulatus are in a third cluster; and L. diadecturus is in a fourth cluster. Among the Xiphinema taxa, 3 subgroups are supported: X. americanum with X. chambersi, X. bakeri with X. diversicaudatum, and X. italiae and X. vuittenezi forming a sister group with X. index. The relationships observed in this study correspond to previous genera and species defined by morphology.     

Aspects of Biology and Development of Xiphinema americanum and Related Species

Identification of Xiphinema americanum-group nematodes is based on relatively subtle morphological and morphometric differences, many of which overlap. The significance and importance of these separations cannot be assessed without a basic understanding of the biological differences between species. Currently, information is accumulating on Xiphinema biology, development, and genetics that will help to confirm or refute the current systematics of species in this group. Recently, it was demonstrated that Xiphinema species pass through either three or four juvenile stages before becoming adults. This new and fundamental information divides the genus and the X. americanum group into subgroups based on their developmental evolution and provides new insight into the taxonomy and systematic positions of the species.     

Xiphinema krugi,Species Complex or Complex of Cryptic Species?

Fourteen morphologically putative populations of X. krugi were clearly separated into four different profiles by RFLP analysis (Alu I and Hinf I), sequencing of the ITS-1 region, and subsequent Maximum Likelihood phylogenetic analyses. These four profiles were further supported by a principal component analysis of morphometric characters that yielded four taxonomic clusters matching those produced by the molecular data. Sequence homology was greater amongst populations that represented the same RFLP profile than between profiles and similar both between representative populations of the RFLP profiles and putative closely related Xiphinema species. This study suggests that X. krugi is a potential species complex comprised of at least four distinct genotypes.     

Seasonal Population Fluctuation of Xiphinema americanum and X. rivesi in New York and Pennsylvania Orchards

The population fluctuation and composition of Xiphinema americanum (sensu stricto) and X. rivesi were studied in a New York apple orchard (only X. americanum present), a Pennsylvania apple orchard (both X. americanum and X. rivesi present), and a Pennsylvania peach orchard (X. americanum, X. rivesi, and X. californicum present). Few clear trends in population fluctuation or composition were observed. The adult female was the predominant stage in most sample periods, and the reproductive period was limited to late spring and early summer. Only a few of the females at any sample period were gravid. All stages were present throughout the year, and all stages overwintered. Eggs in soil were not monitored. In the Pennsylvania apple orchard, X. americanum and X. rivesi were easily separated by morphological characteristics; however, the two species did not display differences in population structure or composition. The predominance of adults, the relatively low reproductive rates, and the association of these species with stable habitats suggest that the life strategies of X. americanum and X. rivesi are K-selected as opposed to r-selected.     

Restriction Fragment Length Polymorphism Separates Species of the Xiphinema americanum Group

The Xiphinema americanum group of species is responsible for vectoring several important virus diseases to perennial crops. Variability of transmission of viruses by different species, and difficulties in separating species by morphometric measurements alone, make it essential to reassess the taxonomic position of several species in the group. The measurement of DNA sequence variability is a sensitive assay that can re-evaluate the separation of species and populations from each other. This study describes how an RFLP approach, in which the restriction sites in transcribed spacers of ribosomal repeats were detected, confirmed the separation of 16 populations of these species into X. americanum, X. rivesi, X. pacificum, and X. bricolensis.     

Morphological Variation in Xiphinema spp. from New York Orchards

Xiphinema specimens were collected from orchards in southeastern, northeastern, and western New York. Total length, distance of vulva from anterior end, spear length (odontostyle plus odontophore), body diameter at vulva, tail length, anal body diameter, and length and diameter of hyaline tail tip were measured on fixed, glycerol-infiltrated adult females. Most specimens were identified as X. americanum or X. rivesi, but one western New York population was identified as X. californicum (a new record for New York). Multivariate analyses indicated that, with one exception, western New York populations of both X. americanum and X. rivesi were smaller and slimmer than their eastern counterparts. Regional differences were generally larger than differences attributed to host species.     

Transmission of Nepoviruses by Xiphinema americanum-group Nematodes

The transmission of North American nepoviruses by putative species belonging to the Xiphinema americanum-group is reviewed. Xiphinema americanum sensu stricto, X. californicum, and X. rivesi each transmit cherry rasp leaf (CRLV), tobacco ringspot (TobRSV), and tomato ringspot nepovirus (TomRSV), and X. bricolensis is a vector of TomRSV. The apparent lack of specificity in the transmission of North American nepoviruses by X. americanum-group species markedly contrasts with the specific associations between European nepoviruses and their vector nematode species. Two complementary projects are described examining the taxonomic identity of putative species in the X. americanum-group, their morphological and genetic relationships, their ontogeny, and their ability to transmit viruses.     

Ribosomal and Mitochondrial DNA Analyses of Xiphinema americanum-Group Populations

The 18S ribosomal DNA (rDNA) and cytochrome oxidase I region of mitochondrial DNA (mtDNA) were sequenced for 24 Xiphinema americanum-group populations sourced from a number of geographically disparate locations. Sequences were subjected to phylogenetic analysis and compared. 18S rDNA strongly suggested that only X. pachtaicum, X. simile (two populations) and a X. americanum s.l. population from Portugal were different from the other 20 populations studied, whereas mtDNA indicated some heterogeneity between populations. Phylogenetically, based on mtDNA, an apparent dichotomy existed amongst X. americanum-group populations from North America and those from Asia, South America and Oceania. Analyses of 18S rDNA and mtDNA sequences underpin the classical taxonomic issues of the X. americanum-group and cast doubt on the degree of speciation within the X. americanum-group.     

Morphological Variation among 23 Xiphinema americanum Populations

Morphometrics of 23 United States populations of Xiphinema americanum sensu lato, sharing the characteristics of an offset lip region and conoid tail, were examined and analyzed statistically by canonical discriminant analysis (CDA). Specimens were collected from Arkansas, Georgia, Tennessee, Mississippi, Florida, Oklahoma, California, and North Dakota. Eleven measurements and body ratios obtained from female specimens were used in the analysis. Xiphinema americanum, X. bricolensis, X. californicum, X. citricolum, X, intermedium, X. tarjanense, and X. thornei, and one undescribed species were identified among the 23 populations. Three groups -- X. americanum-group, X. californicum-group, and X. intermedium-group (X. intermedium and X. tarjanense) -- were formed and four populations belonging to four different species were separated consistently from these groups in CDA scatterplots of the 23 populations. Composition of the groups was somewhat related to the geographical origins of the populations in the groups. A population from California had morphometrics intermediate between X. americanum and X. californicum. Separation between the X. americanum-group and X. californicum-group in the CDA scatterplots was not as distinct as that between them and the X. intermedium-group or between any of the three groups and the four single outlying populations.     

First report,morphological and molecular characterization of Xiphinema elongatum and X. pachtaicum (Nematoda,Longidoridae) from Ethiopia

A total of six soil samples were collected around rhizosphere of citrus plants during 2010 from Melkassa Agricultural Research Center experimental station, Ethiopia. From these samples two most important ecto-plant parasitic nematodes of the genus Xiphinema were found and analysed. The genus Xiphinema is a large group of the phylum nematoda which constitutes more than 260 species. They are polyphagous root- ectoparasites of many crop plants and some species of this genus cause damage by direct feeding on root tips and transmit nepoviruses. The delimitation and discrimination of two species in the genus is presented, described herein as Xiphinema elongatum and Xiphinema pachtaicum. Morphological and morphometric data were done using light microscopy and results of both species were fit within the previously described nematode species of Xiphinema elongatum and Xiphinema pachtaicum. 18S rDNA were analysed using Bayesian inference (BI) method to reconstruct phylogenetic relationships of the studied Xiphinema sp. ({"type":"entrez-nucleotide","attrs":{"text":"KP407872","term_id":"806981416","term_text":"KP407872"}}KP407872 Xiphinema elongatum and {"type":"entrez-nucleotide","attrs":{"text":"KP407873","term_id":"806981417","term_text":"KP407873"}}KP407873 Xiphinema pachtaicum) with other Xiphinema species. The 18S rDNA sequence of Xiphinema pachtaicum was alike to previously described species from the GenBank but Xiphinema elongatum exhibited very small levels of nucleotides differences (0.4%) which might be possible intra-specific divergence. Though this region of rDNA has less resolution on complex species, its combination with morphological and morphometric analyses, suggests these species as Xiphinema elongatum and Xiphinema pachtaicum with the GenBank accession number of {"type":"entrez-nucleotide","attrs":{"text":"KP407872","term_id":"806981416","term_text":"KP407872"}}KP407872 and {"type":"entrez-nucleotide","attrs":{"text":"KP407873","term_id":"806981417","term_text":"KP407873"}}KP407873, respectively. Short notes, morphological measurements, illustrations, and molecular data are given to these species. These species are reported for the first time from Ethiopia and it provides new geographical information of these organisms.     

Phylogenetic Relationships Among Selected Heteroderoidea Based on 18S and ITS Ribosomal DNA

In a study of relationships among selected cyst-forming and noncyst-forming species of Heteroderoidea, combined sequences comprised of DNA from part of the conserved 18S ribosomal RNA gene (rDNA) plus the complete ITS rDNA segment were more similar to analyses based on the ITS data alone than to analyses based on the 18S data alone. One of the two noncyst-forming species, Ekphymatodera thomasoni, grouped with cyst-forming species of Heteroderoidea. Bilobodera flexa, also a noncyst-forming species, was separated from all the other taxa by a long branch. Afenestrata koreana, with a weakly sclerotized cyst, grouped closely with H. bifenestra. These observations suggest that phylogenetic analyses using molecular data may aid in our understanding of the evolution of cyst formation in nematodes, including the possibility of secondary loss. The usefulness of molecular phylogenetic analyses in nematodes may depend more on the particular selection of taxa than on mere addition of data from additional genes.     

Molecular characterization of major and minor rDNA repeats and genetic variability assessment in different species of mahseer found in North India

Relationship among the mahseer species (Family: Cyprinidae) has long been debated in fish systematics. Present study concentrates on the nature of the phylogenetic relationship among the five mahseer species using the sequence of major ribosomal DNA (45S rDNA). We have covered rDNA sequence of approximately 5.2 kb per individual, 26.0 kb per species and 130.0 kb as a whole. We also characterized the 45S and 5S rDNA regions with respect to their nucleotide composition. For phylogenetic analyses, nucleotide sequences were divided into four datasets. First and second datasets contained 18S rDNA and ITS1 sequence, whereas third and fourth datasets consisted of ITS2 and complete 18S-ITS1-5.8S-ITS2-28S, respectively. The NJ tree was constructed for all the datasets. The mahseer species under study formed a monophyletic group well separated from the outgroup species. Similarly, the individuals of Neolissochilus hexagonolepis form monophyletic group with Tor species, indicating Neolissochilus as a sister genus of Tor. The findings from the present study provide greater insights into taxonomic status of mahseer, and set the stage for future investigations dealing with phylo-geography, taxonomy, conservation and co-evolution within this interesting and important group of fish.     

Observations on the Feeding and Symptomatology of Xiphinema and Longidorus on Selected Host Roots

In vitro feeding of Xiphinema brevicolle, X. index and Longidorus africanus on roots of host seedlings is described. Both Xiphinema spp. fed mainly along roots rather than at tips and up to several days at a single site. Feeding of L. africanus was confined to root tips and lasted up to 15 min. No visible short term reaction of roots parasitized by the Xiphinema spp. could be discerned, but both swelling and cessation of growth of root tips were observed within 20 hr after feeding by L. africanus. Long-term (12-month) symptoms on roots of several host plants caused by cultured populations of X. brevicolle, X. index, X. italiae, L. africanus and L. brevicaudatus are described. All the Xiphinema spp. caused a thinning and distinct darkening of root systems and, at some sites, a breakdown of the cortex. Both species of Longidorus caused stubby and swollen root tips. Root symptom severity was in proportion to nematode population levels.     

Effect of Three Plant Species on Population Densities of Xiphinema americanum and X. rivesi

A taxonomic revision of the Xiphinema americanum species complex has necessitated a reexamination of the host range of species in the complex before recommendations can be made with confidence on the likelihood that specific crops will be damaged. Toward this end, populations of X. americanum and X. rivesi collected from apple orchards in eastern and western New York state were evaluated after 3 months in pots planted with cucumber, apple, or dandelion seedlings. Eastern and western New York populations of both nematode species declined on cucumber but increased to similar final densities on apple and dandelion.     

Distribution of Xiphinema americanum and Related Species in North America

All species of the Xiphinema americanum-group and their synonyms are listed. The North American species reported are listed by state or province. Among these species, X. rivesi has the most widely reported distribution. Six species (X. diffusum, X. floridae, X. laevistriatum, X. luci, X. shell, and X. tarjanense) have been reported from only Florida. The reports of X. pachtaicum, X. sheri, and X. luci did not include morphometrics and need to be confirmed; X. brevicolle from California was identified before Lamberti and Bleve-Zacheo described 15 new species in 1979 and similarly needs to be confirmed. Because of the proliferation of species in this group, reports of X. americanum (sensu stricto) before 1979 are questionable. Extraction techniques for longidorids are discussed.     

Characterization of the Cystoid Nematode Meloidoderita kirjanovae (Nemata: Sphaeronematidae) from Southern Italy

A population of the cystoid nematode Meloidoderita kirjanovae was detected parasitizing water mint (Mentha aquatica) in southern Italy. The morphological identification of this species was confirmed by molecular analysis using the internal transcribed spacer 1 (ITS1) and 5.8S gene sequences of nuclear ribosomal DNA (rDNA), which clearly separated it from the closely related species Meloidoderita polygoni. A phylogenetic analysis of M. kirjanovae with species of related genera was conducted using sequences of the D2-D3 expansion segments of the 28S nuclear ribosomal RNA gene. The resulting phylogenetic tree was congruent with trees from an extended dataset for Criconematina and Tylenchida. The basal position of the genus Meloidoderita together with Sphaeronema within the Criconematina clade in this tree may indicate their close relationships. The anatomical changes induced by M. kirjanovae population from Italy in water mint were similar to those reported for a nematode population infecting roots of M. longifolia in Israel. Nematode feeding caused the formation of a stellar syncytium that disorganized the pericycle and vascular root tissues.     

Molecular perspective on the American transisthmian species of Macrobrachium (Caridea,Palaemonidae)

The closure of the Isthmus of Panama (about 3.1 million years ago) separated previously continuous populations and created two groups of extant species, which live now in the Pacific and Atlantic drainage systems. This relatively recent event was a trigger to diversification of various species in the Neotropics, nonetheless there are exemplars that do not show sufficient morphologic variability to separate them by traditional morphological tools. About 60 years ago, some freshwater decapod species with high morphological similarity were separate by previous researchers, based on geographical distribution, in Pacific and Atlantic and considered as “sister species”. However, the complete isolation of these prawns by this geographical barrier is questionable, and it has generated doubts about the status of the following transisthmian pairs of sibling species: Macrobrachium occidentale × Macrobrachium heterochirus, Macrobrachium americanum × Macrobrachium carcinus, Macrobrachium digueti × Macrobrachium olfersii, Macrobrachium hancocki × Macrobrachium crenulatum, Macrobrachium tenellum × Macrobrachium acanthurus and Macrobrachium panamense × Macrobrachium amazonicum. Here we evaluated the relation among these pairs of sibling species in a molecular phylogenetic context. We generated 95 new sequences: 26 sequences of 16S rDNA, 25 of COI mtDNA and 44 of 18S nDNA. In total, 181 sequences were analyzed by maximum likelihood phylogenetic method, including 12 Macrobrachium transisthmian species, as well as seven other American Macrobrachium species, and two other palaemonids. Our analysis corroborated the morphological proximity of the sibling species. Despite the high degree of morphological similarities and considerable genetic diversification encountered among the transisthmian sister species, our data support the conclusion that all species included in sibling groups studied herein are valid taxonomic entities, but not all pairs of siblings form natural groups.     

Scanning Electron Microscopy of Xiphinema,Longidorus, and Californidorus Stylet Morphology

Stylet ultrastructure of five Xiphinema, four Longidorus, and three Californidorus species was compared by scanning electron microscopy. Morphological differences were seen in the odontophores and odontostyle bases between the genera and some of the species. All Xiphinema studied had well-developed odontophore flanges; the Longidorus species lacked flanges, except for weakly developed ones in L. diadecturus; and none of the Californidorus had flanges. Three sinuses were present in the odontophores of all species. The sinuses varied in length depending upon species. In Xiphinema and Californidorus the odontostyle bases had distinct overlapping collars, but in Longidorus the collars were absent except for L. diadecturus. The odontostyle-odontophore junction from a lateral view appeared as a slanted transverse line in all the species, but in a dorsal view of Xiphinema and Californidorus it was V-shaped. Dorsal longitudinal seams of the odontostyle and odontophore were observed in all the species. The dorsally located odontostyle aperture was ca. 1 μm from the anterior end in all species, except in one Longidorus sp. it was ca. 4 μm from the end.     

Morphological Comparisons Between Xiphinema rivesi Daimasso and X. americanum Cobb Populations from the Eastern United States

Though in the past Xiphinema americanum has been the most commonly reported dagger nematode in the eastern United States, our studies revealed the presence in Pennsvlvania of a previously unrecognized and unreported species related to X. americanum, Morphometric data and photomicrographs establish the identity of this form as X. rivesi and show expected variations in populations of this species from various locations. Similar data and illustrations are given for X. americanum populations from Pennsylvania and other areas, showing variations and relationships. Xiphinema rivesi is widely distributed in the fruit producing area of south-central Pennsylvania and is also reported herein from raspberry in Vermont and apple in Maryland and New York. This species is frequently found in fruit growing areas of Pennsylvania associated with tomato ringspot virus-induced diseases and is also found associated with corn, bluegrass sod, and alfalfa.