Barcode characteristics: This dataset is comprised of 100 18S barcode MOTUs derived from 214 sequences from nematodes in the suborder Criconematina (). The ClustalW alignment is 602 nucleotides in length which includes 10 hypothesized sites of nucleotide insertion or deletion (indels). There are 470 (78%) invariant and 132 polymorphic nucleotide sites in the dataset. Among the polymorphic nucleotide sites, 56 (42%) are singletons, positions where a single MOTU has a nucleotide not shared by any others in the dataset.
Barcode species analysis: The dataset includes 25 nominal species identified by the authors through microscopic examinations of morphological characteristics. A maximum likelihood tree for the 100 MOTUs is presented in . Four clusters with moderate support values (0.80-0.93) have been identified and were labeled A-D for character-based barcode analysis.
Fig. 1 Maximum likelihood tree of Criconematina 18S 3’ MOTUs. Shaded clades A-D were analyzed separately by character-based barcode analysis. Species binomials followed by GB were sequences added to the analyses from GenBank. Images and measurements (more ...)
Within clade A, there are nine morphologically identified nominal species not considering GenBank entries (, ). Included in this clade are species that morphologically fall within the genera Ogma, Xenocriconemella, Criconema, and Hemicriconemoides. Five of the Ogma species possessed morphological characters that permitted assignment to known species. However, neither phylogenetic analysis nor character-based barcode analysis recognized all Ogma MOTUs as collectively comprising a natural group exclusive of the other genera in the clade. Ogma decalineatum and O. octangulare shared a T at nucleotide 67 to the exclusion of all other MOTUs in clade A (). Another nucleotide character (C) at position 391 provides evidence for relatedness of these two species to O. seymouri. The O. menzeli MOTU from Tennessee (M72) differs by two nucleotides from the European O. menzeli in GenBank (M73). M76 is a broadly distributed MOTU, one of only two MOTUs found in both Costa Rica and the United States. Additionally, it shares 100% identity with GenBank accession EU669918, an O. cobbi reported from Europe. Morphologically, the adult females that represent M76 include a range of phenotypes, particularly in the arrangement of scales on the adult female cuticle.
Xenocriconemella macrodora is represented by 12 specimens and three MOTUs (M98, M99, M100) collected from five U.S. states. There are four diagnostic nucleotide sites, including two insertions, which are observed in every specimen of this species. These are found at nucleotide positions 349, 352, 363, and 364. Hemicriconemoides wessoni was collected at two sites in Florida, one site within 60 miles of the type locality. Three MOTUs were observed for this species, each diagnosable by nucleotides T and G at positions 362 and 365 respectively. Criconema permistum and C. sphagni were represented by one and three specimens respectively, each containing a single, unique fixed nucleotide. Other Criconema species in clade A are not united by shared derived characters, reflecting a lack of phylogenetic support for the genus.
Clade B, with the exception of a single MOTU (M4), is exclusively represented by Discocriconemella limitanea
from Costa Rica (). The clade is well-supported phylogenetically. D. limitanea
is represented by 12 specimens and 11 MOTUs which break into two discrete subgroups. There are six nucleotide sites that separate the two subgroups. Morphologically, however, there are no characters that appear to discriminate between the subgroups, and both subgroups are found in Las Cruces and La Selva Biological Research Stations, geographically distinct rainforest habitats of Costa Rica. MOTU M4 was recovered from cultivated passionfruit in Costa Rica and conforms morphologically to Mesocriconema crenatum
) De Grisse & Loof, 1965.
Clade C includes six nominal species identified by morphology (). Both phylogenetic analysis and character-based barcode analysis support Mesocriconema rusticum
as diagnosable species within this clade. Nucleotide sites at 472 and 488 diagnose M. rusticum
, and an additional two synapomorphic characters at sites 46 and 503 support a sister group relationship with M. ornatum
. Mesocriconema rusticum
was represented by 6 specimens and two MOTUs collected from 5 U.S. states. Four nucleotide sites, 31, 34, 56, and 59 diagnose M. curvatum
. MOTU M63 was represented by 18 specimens and includes two morphologically identifiable species M. xenoplax
and Discocriconemella inarata.
A previous paper has addressed the more detailed taxonomy of these two species (Powers et al., 2010
). There are no diagnosable characters in this 18S barcode for discrimination between M. xenoplax
and D. inarata
. Three additional MOTUs, M65, M66 and M67 from GenBank have been identified as M. xenoplax
from Europe. Mesocriconema discus
(M57) was collected at its type locality in South Dakota, however there were no discrete nucleotide characters that could be considered as diagnosable nucleotide sites.
Table 4 Clade C polymorphic and diagnostic nucleotide positions with diagnostic characters. Diagnostic nucleotides are those shared by all individuals of a species and not found in any other species. The diagnostic nucleotide characters are shaded with a bold (more ...)
Clade D was largely comprised of Hemicycliophora species, the two related sheath genera Hemicaloosia and Loofia, Lobocriconema, and Criconemoides species (). Criconemoides annulatus (M16), represented by two specimens from the Rocky Mountains in Colorado, possessed three diagnostic nucleotide sites. Lobocriconema thornei (M51) and a closely related Lobocriconema species (M50) had four synapomorphic sites, and each was diagnosable by a single autapomorphic site. Among the sheath genera, two synapomorphic nucleotide sites at 43 and 47 united all specimens. Hemicycliophora gracilis, represented by a single MOTU collected in Colorado and Nebraska, possessed five autapomorphic diagnostic sites. Hemicycliophora typica and the two species from GenBank in this dataset did not possess diagnosable nucleotides in the 18S barcode.
Table 5 Clade D polymorphic and diagnostic nucleotide positions with diagnostic characters. Diagnostic nucleotides are those shared by all individuals of a species and not found in any other species. The diagnostic nucleotide characters are shaded with a bold (more ...)
Five notable, diagnosable species in the 100-MOTU dataset did not fall within clades A-D (). Bakernema inaequale
is a species endemic to North America and immediately recognizable by its irregularly arranged, membranous cuticular scales. Seven specimens from Tennessee and Connecticut shared a single MOTU (M1) and were diagnosable in the full dataset by an A at nucleotide position 63. Criconemoides informis
(M17) had two diagnostic nucleotides: an A and T at positions 343 and 357, respectively. Criconemoides inusitatus
(M18), collected from the type locality in Ames, IA and from Delaware, had a single diagnostic nucleotide site at position 365. A species morphologically conforming to Neolobocriconema serratum
(M68) collected from Missouri and Nebraska, had a single diagnostic site at position 360. Three MOTUs (M94, M95, M96) represented the unusual criconematid nematode Tylenchocriconema alleni
, a species known solely from epiphytic bromeliads in the new world tropics (Raski and Siddiqui, 1975
). Two nucleotide sites at 347 and 348 were diagnostic for the three MOTUs.
Table 6 Diagnostic nucleotide positions for species not included in clades A-D. These species compared against the entire Criconematina data set. Numbers after taxon labels refer to number of specimens examined. Numbering of the nucleotide position starts with (more ...)