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.     

Phylogenetic Relationships Among Xiphinema and Xiphidorus Nematode Species from Brazil Inferred from 18S rDNA Sequences

Maximum likelihood trees produced from 18S rDNA sequences separated 14 Xiphinema and five Xiphidorus nematode species from Brazil into distinct groups that concurred with their current morphological taxonomic status. Species belonging to the X. americanum group (X. brevicolle, X. diffusum, X. oxycaudatum, and X. peruvianum) formed a single group that was clearly separated from the other Xiphinema species. As with previous taxonomic studies that noted only minor morphological differences between putative X. americanum group species, separation of these species based upon 18S rDNA sequences was inconclusive. Thus it is probable that instead of comprising distinct species, the X. americanum group may in fact represent numerous morphotypes with large inter- and intra- population morphological variability that may be environmentally driven. Within the cluster representing non X. americanum group species, there was little statistical support to clearly separate species. However, three subgroups, comprising (i) the X. setariae/vulgare complex, (ii) X. ifacolum and X. paritaliae, and (iii) X. brasiliense and X. ensiculiferum were well resolved.     

Inter- and Intraspecific Variation in Wild-type and Single Female-derived Populations of Xiphinema americanum-group Nematodes

Ten populations of Xiphinema americanum-group nematodes were reared from individual females to evaluate inter- and intraspecific variation under identical host and environmental conditions. Data indicated that morphometric variability of X. americanum was the result of genetic variation rather than phenotypic plasticity and that genetic heterogeneity was greater than previously thought. Morphometrics of single female derived (SFD) populations identified different genotypes present in the field populations. Stylet length was the least variable morphometric character of SFD populations, but collectively stylet measurements of all individuals formed an uninterrupted continuum ranging from 107-148 μm. Range and frequency of stylet measurements of field populations could be accounted for by the relative proportion of different genotypes in the population. Nine SFD populations were identified as X. americanum sensu stricto, and one SFD population was similar to X. californicum.     

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.     

Morphometric Evidence for Three Juvenile Stages in Some Species of Xiphinema americanum sensu lato

One to two hundred nematodes from each of seven Xiphinema americanum-group populations were measured to determine the range of stylet and body lengths for juveniles and adults. First-stage juveniles were identified by the position of the replacement odontostyle (i.e., the tip of the replacement odontostyle overlapped the base of the odontophore). Nematodes were identified as second stage if the functional odontostyle was the same length as the replacement odontostyle of the first stage. Subsequent stages were similarly identified by establishing the range of corresponding replacement and functional odontostyle lengths. In all populations examined, this procedure created natural divisions that clearly grouped nematodes by stylet and body length. Presumably these groups identified all juvenile and adult stages. Populations of X. americanum, X. rivesi, and X. californicum from the United States had three juvenile stages, but a population of X. pachtaicum from Bulgaria had four juvenile stages.     

Diversity of Xiphinema americanum-group Species and Hierarchical Cluster Analysis of Morphometrics

Of the 39 species composing the Xiphinema americanum group, 14 were described originally from North America and two others have been reported from this region. Many species are very similar morphologically and can be distinguished only by a difficult comparison of various combinations of some morphometric characters. Study of morphometrics of 49 populations, including the type populations of the 39 species attributed to this group, by principal component analysis and hierarchical cluster analysis placed the populations into five subgroups, proposed here as the X. brevicolle subgroup (seven species), the X. americanum subgroup (17 species), the X. taylori subgroup (two species), the X. pachtaicum subgroup (eight species), and the X. lambertii subgroup (five species).     

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.     

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 and Molecular Evaluation of a Meloidogyne hapla Population Damaging Coffee (Coffea arabica) in Maui,Hawaii

An unusual population of Meloidogyne hapla, earlier thought to be an undescribed species, was found causing large galls, without adventitious roots, and substantial damage to coffee in Maui, Hawaii. Only in Brazil had similar damage to coffee been reported by this species. Unlike M. exigua from South and Central America, this population reproduced well on coffee cv. Mokka and M. incognita-susceptible tomato but poorly on tomato with the Mi resistance gene. Characterization included SEM images, esterase isozymes, and five DNA sequences: i) the D3 segment of the large subunit (LSU-D3 or 28S) rDNA, ii) internal transcribed spacer (ITS-1) rDNA, iii) intergenic spacer (IGS) rDNA, iv) the mitochondrial interval from cytochrome oxidase (CO II) to 16S mtDNA, and v) the nuclear gene Hsp90. Sequences for ITS-1, IGS, and COII were similar to other M. hapla populations, but within species ITS-1 variability was not less than among species. One LSU-D3 haplotype was similar to a previously analyzed population with two minor haplotypes. Hsp90 exhibited some variation between Maryland and Hawaiian populations distinct from other species. Females were narrow with wide vulval slits, large interphasmidial distances, and more posterior excretory pores; 20% of perineal patterns had atypical perivulval lines. Males had a low b ratio (<12 µm). Juveniles had a short distance between stylet and dorsal gland orifice. Juvenile body length was short (<355 µm) and was different between summer and winter populations.     

Differentiation of Species and Populations of Aphelenchoides and of Ditylenchus angustus Using a Fragment of Ribosomal DNA

The polymerase chain reaction (PCR) was used to amplify a fragment of the ribosomal DNA (rDNA) from species and undescribed populations of Aphelenchoides and Ditylenchus angustus. The PCR primers used were based on conserved sequences in the 18S and 26S ribosomal RNA genes of Caenorhabditis elegans. In C. elegans, these primers amplify a 1,292 base pair (bp) fragment, which consists of the two internal transcribed spacers and the entire 5.8S gene. Amplification products from crude DNA preparations of 12 species and populations of Aphelenchoides and from D. angustus ranged in size from approximately 860-1,100bp. Southern blots probed with a cloned ribosomal repeat from C. elegans confirmed the identity of these amplified bands as ribosomal fragments. In addition to the differing sizes of the amplified rDNA fragments, the relative intensity of hybridization with the C. elegans probe indicated varying degrees of sequence divergence between species and populations. In some cases, amplified rDNA from the fungal host was evident. Storage of A. composticola at - 45 C for 2 years did not affect the ability to obtain appropriate amplified products from crude DNA preparations. Amplified rDNA fragments were cut with six restriction enzymes, and the restriction fragments produced revealed useful diagnostic differences between species and some undescribed populations. These results were consistent with previous studies based on morphology and isoenzymes. Three undescribed populations of Aphelenchoides were found to be different from all the species examined and from each other.     

Molecular Analysis of the Freshwater Prawn Macrobrachium olfersii (Decapoda,Palaemonidae) Supports the Existence of a Single Species throughout Its Distribution

Macrobrachium olfersii is an amphidromous freshwater prawn, widespread along the eastern coasts of the Americas. This species shows great morphological modifications during ontogenesis, and several studies have verified the existence of a wide intraspecific variation. Because of this condition, the species is often misidentified, and several synonyms have been documented. To elucidate these aspects, individuals of M. olfersii from different populations along its range of distribution were investigated. The taxonomic limit was established, and the degree of genetic variability of this species was described. We extracted DNA from 53 specimens of M. olfersii, M. americanum, M. digueti and M. faustinum, which resulted in 84 new sequences (22 of 16S mtDNA, 45 of Cythocrome Oxidase I (COI) mtDNA, and 17 of Histone (H3) nDNA). Sequences of three genes (single and concatenated) from these species were used in the Maximum Likelihood and Bayesian Inference phylogenetic analyses and COI sequences from M. olfersii were used in population analysis. The genetic variation was evaluated through the alignment of 554 bp from the 16S, 638 bp from the COI, and 338 bp from the H3. The rates of genetic divergence among populations were lower at the intraspecific level. This was confirmed by the haplotype net, which showed a continuous gene flow among populations. Although a wide distribution and high morphological intraspecific variation often suggest the existence of more than one species, genetic similarity of Caribbean and Brazilian populations of M. olfersii supported them as a single species.     

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.     

Molecular systematics of the genus Troglophilus (Rhaphidophoridae,Orthoptera) in Turkey: mitochondrial 16S rDNA evidences

This study focuses on the evolutionary relationships among Turkish species of the cave cricket genus Troglophilus.Fifteen populations were studied for sequence variation in a fragment (543 base pairs) of the mitochondrial DNA (mtDNA) 16S rDNA gene (16S) to reconstruct their phylogenetic relationships and biogeographic history. Genetic data retrieved three main clades and at least three divergent lineages that could not be attributed to any of the taxa known for the area. Molecular time estimates suggest that the diversification of the group took place between the Messinian and the Plio-Pleistocene.     

Assessing Nuclear and Mitochondrial DNA Sequence Variation Within Steinernema (Rhabditida: Steinernematidae)

DNA sequence analysis was used to characterize the nuclear ribosomal DNA ITS1 region and a portion of the COII and 16S rDNA genes of the mitochondrial genome from Steinernema entomopathogenic nematodes. Nuclear ITS1 nucleotide divergence among seven Steinernema spp. ranged from 6 to 22%, and mtDNA divergence among five species ranged from 12 to 20%. No intraspecific variation was observed among three S. feltiae strains. Phylogenetic analysis of both nuclear and mitochondrial DNA sequences confirms the existing morphological relationships of several Steinernema species. Both the rDNA ITS1 and mtDNA sequences were useful for resolving relationships among Steinernema taxa.     

The Mitochondrial Genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): Considerable Economization in the Length and Structural Features of Encoded Genes

The complete sequence of the mitochondrial genome of the plant parasitic nematode Xiphinema americanum sensu stricto has been determined. At 12626bp it is the smallest metazoan mitochondrial genome reported to date. Genes are transcribed from both strands. Genes coding for 12 proteins, 2 rRNAs and 17 putative tRNAs (with the tRNA-C, I, N, S1, S2 missing) are predicted from the sequence. The arrangement of genes within the X. americanum mitochondrial genome is unique and includes gene overlaps. Comparisons with the mtDNA of other nematodes show that the small size of the X. americanum mtDNA is due to a combination of factors. The two mitochondrial rRNA genes are considerably smaller than those of other nematodes, with most of the protein encoding and tRNA genes also slightly smaller. In addition, five tRNAs genes are absent, lengthy noncoding regions are not present in the mtDNA, and several gene overlaps are present. [Reviewing Editor: Dr. Yues van de Peer] F. Lamberti: Deceased, 2004     

Incomplete barriers to mitochondrial gene flow between pheromone races of the North American pine engraver,Ips pini (Say) (Coleoptera,Scolytidae)

The pine engraver Ips pini (Say) is known to include three pheromone races, but gene flow between these races has not been investigated. We used maternally inherited mitochondrial DNA (mtDNA) variation to infer gene flow between 22 widely distributed North American populations of I. pini for a total of 217 individuals, based on 354 bp of the cytochrome oxidase I gene. Gene flow was estimated cladistically as migrants per generation (Nm) and as haplotype variation between populations (N_st). Three distinct mtDNA haplotype lineages, generally corresponding to eastern (I), Rocky Mountain (II) and western (III) regions of North America, were resolved with a total of 34 distinct I. pini haplotypes. The distributions of these lineages were largely congruent with the geographical ranges of the ''New York'', ''California'' and ''Idaho–Montana'' pheromone races. Only individuals with lineage I mtDNA were observed among eastern populations, whereas individuals with lineage II or III mtDNA predominated among western populations. Gene flow (Nm and N_st) was generally moderate between all populations. However, the presence of lineage I mtDNA on the eastern side of western North America and the absence of lineage II and III mtDNA in eastern North America suggest directional gene flow from east to west. These results indicate that female-controlled assortative mating among pheromone races may disrupt gene flow between conspecifics, reflecting incomplete pre-mating barriers.     

Vector Capability of Xiphinema americanum sensu lato in California

Seven field populations of Xiphinema americanum sensu lato from California''s major agronomic areas were tested for their ability to transmit two nepoviruses, including the prune brownline, peach yellow bud, and grapevine yellow vein strains of tomato ringspot virus and the bud blight strain of tobacco ringspot virus. Two field populations transmitted all isolates, one population transmitted all tomato ringspot virus isolates but failed to transmit bud blight strain of tobacco ringspot virus, and the remaining four populations failed to transmit any virus. Only one population, which transmitted all isolates, bad been associated with field spread of a nepovirus. As two California populations of Xiphinema americanum sensu lato were shown to have the ability to vector two different nepoviruses, a nematode taxonomy based on a parsimony of virus-vector relationship is not practical for these populations. Because two California populations of X. americanum were able to vector tobacco ringspot virus, commonly vectored by X. americanum in the eastern United States, these western populations cannot be differentiated from eastern populations by vector capability tests using tobacco ringspot virus.     

Phylogeography of northern Dolly Varden Salvelinus malma (Salmoniformes: Salmonidae) from Asia and North America: An analysis based on the mitochondrial DNA genealogy

Spawning in habitats affected by Pleistocene glacial advances over most of its natural range, northern Dolly Varden Salvelinus malma malma typifies Arctic fauna distributed in northeastern Asia and northwestern North America. We reconstructed a genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of historical events on the phylogeography and contemporary population genetic structure. Analysis of molecular variance partitioned most of the mtDNA variability to the intrapopulation component (72.5%) with much reduced differences between populations (21.1%) and regions (6.4%). Similar patterns of variation apparent from hierarchical diversity and nested clade phylogeographical analysis (NCPA) of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. These findings suggest (1) that demographic history has been influenced by historical range expansions and recent isolation by distance, (2) that present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon’s ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period. The genealogical and NCPA analyses, and mismatch distribution of S. m. malma mtDNA haplotypes do not confirm the assumptions about presence of the two refugia on the territories of the Beringian Land, in which allopatric S. m. malma ancestral populations evolved, and independent origin of the Sea of Okhotsk populations.     

Chromosomal organization of repetitive DNA sequences in Astyanax bockmanni (Teleostei, Characiformes): dispersive location, association and co-localization in the genome

Repetitive DNA sequences constitute a great portion of the genome of eukaryotes and are considered key components to comprehend evolutionary mechanisms and karyotypic differentiation. Aiming to contribute to the knowledge of chromosome structure and organization of some repetitive DNA classes in the fish genome, chromosomes of two allopatric populations of Astyanax bockmanni were analyzed using classic cytogenetics techniques and fluorescent in situ hybridization, with probes for ribosomal DNA sequences, histone DNA and transposable elements. These Astyanax populations showed the same diploid number (2n = 50), however with differences in chromosome morphology, distribution of constitutive heterochromatin, and location of 18S rDNA and retroelement Rex3 sites. In contrast, sites for 5S rDNA and H1, H3 and H4 histones showed to be co-located and highly conserved. Our results indicate that dispersion and variability of 18S rDNA and heterochromatin sites are not associated with macro rearrangements in the chromosome structure of these populations. Similarly, distinct evolutionary mechanisms would act upon histone genes and 5S rDNA, contributing to chromosomal association and co-location of these sequences. Data obtained indicate that distinct mechanisms drive the spreading of repetitive DNAs in the genome of A. bockmanni. Also, mobile elements may account for the polymorphism of the major rDNA sites and heterochromatin in this genus.