Molecular phylogenetic analyses of 113 taxa representing Ascaridida, Rhigonematida, Spirurida and Oxyurida were used to infer a more comprehensive phylogenetic hypothesis for representatives of 'clade III'. The posterior probability of multiple alignment sites was used to exclude or weight characters, yielding datasets that were analysed using maximum parsimony, likelihood, and Bayesian inference methods. Phylogenetic results were robust to differences among inference methods for most high-level taxonomic groups, but some clades were sensitive to treatments of characters reflecting differences in alignment ambiguity. Taxa representing Camallanoidea, Oxyurida, Physalopteroidea, Raphidascarididae, and Skrjabillanidae were monophyletic in all 9 analyses whereas Ascaridida, Ascarididae, Anisakidae, Cosmocercoidea, Habronematoidea, Heterocheilidae, Philometridae, Rhigonematida and Thelazioidea were never monophyletic. Some clades recovered in all trees such as Dracunculoidea and Spirurina included the vast majority of their sampled species, but were non-monophyletic due to the consistent behaviour of one or few 'rogue' taxa. Similarly, 102 of 103 clade III taxa were strongly supported as monophyletic, yet clade III was paraphyletic due to the grouping of Truttaedacnitis truttae with the outgroups. Mapping of host 'habitat' revealed that tissue-dwelling localization of nematode adults has evolved independently at least 3 times, and relationships among Spirurina and Camallanina often reflected tissue predilection rather than taxonomy.

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A phylogenetic analysis of 40 species of Rhabdochona Railliet, 1916, including all 21 valid species in the Americas, resulted in 1733 equally most parsimonious trees and indicates that Rhabdochona is arguably monophyletic. Species from the Americas do not form a monophyletic group, since each of the six clades of Rhabdochona includes species from the Americas and species from other continents. The synapomorphies defining each clade stem from the morphology of the left spicule. Teeth number was consistent in one clade only, suggesting that this character, while useful for taxonomic purposes, is not indicative of phylogeny. Species of Rhabdochona associated with certain host groups, such as salmonids, catostomids and goodeids, do not always form monophyletic assemblages, nor do species associated with smaller discrete areas, such as the Mesa Central of Mexico. This indicates widespread host-switching rather than co-speciation as the main phenomenon in the evolution of this group, at least in the species from the Americas. Phylogenetic patterns reveal an ancient origin for the group that probably pre-dates current continental configurations.

Aim  The phylogeography of Rhabdochona lichtenfelsi, a nematode parasite specific to endemic goodeids in Mexico, is used to infer the biogeographical history of fragmentation and recent evolution of the Mesa Central drainages. Geological history of the west‐central region of Mexico suggests that extant freshwater basins are the result of different vicariant events that fragmented ancient watercourses and lakes within the Mesa Central. Location  Major freshwater river basins of the Mesa Central, Mexico: Ameca, Cotija, Lerma, Rio Verde, Panuco, and lakes Cuitzeo and Zacapu. Methods  Haplotype diversity and phylogeographical structure of 10 populations of R. lichtenfelsi, sampled from the complete range of this species, were analysed with partial sequences of cytochrome c oxidase subunit I (456 bp). Analyses performed included phylogenetic tree estimation methods (neighbour‐joining, maximum parsimony and maximum likelihood), genetic diversity, distance and structure estimates, and nested clade analysis. Results  High overall haplotype diversity, unique haplotypes, and strongly structured populations were found in the basins sampled. Three phylogenetically and demographically identifiable clades were recovered. These clades fit an isolation‐by‐distance model. Significant population expansion was observed for two clades and for the entire population. Time of divergence was estimated as 1.0 and 0.84 Ma for the different clades. Main conclusions  The distribution of R. lichtenfelsi haplotypes does not correspond to the present distribution of the basins of Mesa Central, but instead reflects the distribution of those basins during a recent geological period (Pleistocene). While our current knowledge of the evolution and geographical relationships of the Mesa Central basins comes from studies of freshwater fish encompassing a more ancient history, our results suggest that, during the past million years, old basins and connections existed where today isolated freshwater bodies stand, thus unravelling a novel biogeographical history for the Mesa Central of Mexico.

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