Development and Characterization of 12 Novel Polymorphic Microsatellite Loci for the Mammal Chewing Louse Geomydoecus aurei (Insecta: Phthiraptera) and a Comparison of Next-Generation Sequencing Approaches for Use in Parasitology.

Next-generation sequencing methodologies open the door for evolutionary studies of wildlife parasites. We used 2 next-generation sequencing approaches to discover microsatellite loci in the pocket gopher chewing louse Geomydoecus aurei for use in population genetic studies. In one approach, we sequenced a library enriched for microsatellite loci; in the other approach, we mined microsatellites from genomic sequences. Following microsatellite discovery, promising loci were tested for amplification and polymorphism in 390 louse individuals from 13 pocket gopher hosts. In total, 12 loci were selected for analysis (6 from each methodology), none of which exhibited evidence of null alleles or heterozygote deficiencies. These 12 loci showed adequate genetic diversity for population-level analyses, with 3-9 alleles per locus with an average HE per locus ranging from 0.32 to 0.70. Analysis of Molecular Variance (AMOVA) indicated that genetic variation among infrapopulations accounts for a low, but significant, percentage of the overall genetic variation, and individual louse infrapopulations showed FST values that were significantly different from zero in the majority of pairwise infrapopulation comparisons, despite all 13 infrapopulations being taken from the same locality. Therefore, these 12 polymorphic markers will be useful at the infrapopulation and population levels for future studies involving G. aurei. This study shows that next-generation sequencing methodologies can successfully be used to efficiently obtain data for a variety of evolutionary questions.

Cophylogenetic Reconciliation with ILP.

In this paper, we present an integer linear programming (ILP) approach, called CoRe-ILP, for finding an optimal time consistent cophylogenetic host-parasite reconciliation under the cophylogenetic event model with the events cospeciation, duplication, sorting, host switch, and failure to diverge. Instead of assuming event costs, a simplified model is used, maximizing primarily for cospeciations and secondarily minimizing host switching events. Duplications, sortings, and failure to diverge events are not explicitly scored. Different from existing event based reconciliation methods, CoRe-ILP can use (approximate) phylogenetic branch lengths for filtering possible ancestral host-parasite interactions. Experimentally, it is shown that CoRe-ILP can successfully use branch length information and performs well for biological and simulated data sets. The results of CoRe-ILP are compared with the results of the reconciliation tools Jane 4, Treemap 3b, NOTUNG 2.8 Beta, and Ranger-DTL. Algorithm CoRe-ILP is implemented using IBM ILOG CPLEX Optimizer 12.6 and is freely available from http://pacosy.informatik.uni-leipzig.de/core-ilp.

Host behaviour drives parasite genetics at multiple geographic scales: population genetics of the chewing louse, Thomomydoecus minor.

Pocket gophers and their symbiotic chewing lice form a host-parasite assemblage known for a high degree of cophylogeny, thought to be driven by life history parameters of both host and parasite that make host switching difficult. However, little work to date has focused on determining whether these life histories actually impact louse populations at the very fine scale of louse infrapopulations (individuals on a single host) at the same or at nearby host localities. We used microsatellite and mtDNA sequence data to make comparisons of chewing-louse (Thomomydoecus minor) population subdivision over time and over geographic space where there are different potential amounts of host interaction surrounding a zone of contact between two hybridizing pocket-gopher subspecies. We found that chewing lice had high levels of population isolation consistent with a paucity of horizontal transmission even at the very fine geographic scale of a single alfalfa field. We also found marked genetic discontinuity in louse populations corresponding with host subspecies and little, if any, admixture in the louse genetic groups even though the lice are closely related. The correlation of louse infrapopulation differentiation with host interaction at multiple scales, including across a discontinuity in pocket-gopher habitat, suggests that host behaviour is the primary driver of parasite genetics. This observation makes sense in light of the life histories of both chewing lice and pocket gophers and provides a powerful explanation for the well-documented pattern of parallel cladogenesis in pocket gophers and chewing lice.

Characterization of 17 novel polymorphic microsatellite loci in the mammal chewing louse Geomydoecus ewingi (Insecta: Phthiraptera) for population genetic analyses.

We report 17 novel microsatellite loci in the parasitic chewing louse Geomydoecus ewingi, a common parasite of the pocket gopher, Geomys breviceps . Thirty-three G. ewingi individuals from 1 geographic locality and 3 pocket gopher hosts (populations) were genotyped at each locus. The number of alleles per locus ranged from 3 to 13. Observed heterozygosity ranged from 0.182 to 0.788. Four to 6 loci per louse population fell outside of Hardy-Weinberg expectations (HWE) and examination of population structure also revealed substantial homozygote excess as well as significant structure among louse populations. These findings are likely the consequence of biological characteristics of the lice (low dispersal abilities, population bottlenecks, etc.), which can result in inbreeding. Notably, when all louse individuals were analyzed together as 1 population, a Wahlund effect was detected, supporting that louse populations are restricted to 1 host individual. The microsatellite markers characterized in this study will be useful in future studies exploring the population dynamics in host-parasite systems, potentially yielding a better understanding of the processes underlying symbiotic associations.

Four events of host switching in Aspidoderidae (Nematoda) involve convergent lineages of mammals.

The Great American Interchange resulted in the mixing of faunistic groups with different origins and evolutionary trajectories that underwent rapid diversification in North and South America. As a result, groups of animals of recent arrival converged into similar habits and formed ecological guilds with some of the endemics. We present a reconstruction of the evolutionary events in Aspidoderidae, a family of nematodes that infect mammals that are part of this interchange, i.e., dasypodids, opossums, and sigmodontine, geomyid, and hystricognath rodents. By treating hosts as discrete states of character and using parsimony and Bayesian inferences to optimize these traits into the phylogeny of Aspidoderidae, we reconstructed Dasypodidae (armadillos) as the synapomorphic host for the family. In addition, 4 events of host switching were detected. One consisted of the switch from dasypodids to hystricognath rodents, and subsequently to geomyid rodents. The remaining set of events consisted of a switch from dasypodids to didelphid marsupials and then to sigmodontine rodents. The reconstruction of the ancestral distribution suggests 3 events of dispersal into the Nearctic. Two of these invasions would suggest that 2 different lineages of dasypodid parasites entered the Northern Hemisphere at different times, which is consistent with the presence of 2 lineages of armadillos in Mexico.

Cophylogeny on a fine scale: Geomydoecus chewing lice and their pocket gopher hosts, Pappogeomys bulleri.

Many species of pocket gophers and their ectoparasitic chewing lice have broadly congruent phylogenies, indicating a history of frequent codivergence. For a variety of reasons, phylogenies of codiverging hosts and parasites are expected to be less congruent for more recently diverged taxa. This study is the first of its scale in the pocket gopher and chewing louse system, with its focus entirely on comparisons among populations within a single species of host and 3 chewing louse species in the Geomydoecus bulleri species complex. We examined mitochondrial DNA from a total of 46 specimens of Geomydoecus lice collected from 11 populations of the pocket gopher host, Pappogeomys bulleri. We also examined nuclear DNA from a subset of these chewing lice. Louse phylogenies were compared with a published pocket gopher phylogeny. Contrary to expectations, we observed a statistically significant degree of parallel cladogenesis in these closely related hosts and their parasites. We also observed a higher rate of evolution in chewing louse lineages than in their corresponding pocket gopher hosts. In addition, we found that 1 louse species (Geomydoecus burti) may not be a valid species, that subspecies within G. bulleri are not reciprocally monophyletic, and that morphological and genetic evidence support recognition of a new species of louse, Geomydoecus pricei.

New species of Arostrilepis (Eucestoda: Hymenolepididae) in members of Cricetidae and Geomyidae (Rodentia) from the western Nearctic.

Abstract : Specimens originally identified as Arostrilepis horrida from the Nearctic are revised, contributing to the recognition of a complex of cryptic species distributed across the Holarctic region. Previously unrecognized species are described based on specimens in cricetid (Neotominae) and geomyid rodents. Arostrilepis mariettavogeae n. sp. in Peromyscus californicus from Monterey County, California and Arostrilepis schilleri n. sp. in Thomomys bulbivorus from Corvallis, Oregon are characterized. Consistent with recent studies defining diversity in the genus, form, size, and spination (pattern, shape, and size) of the cirrus are diagnostic; species are further distinguished by the relative position and length of the cirrus sac and arrangement of the testes. Species of Arostrilepis have not previously been described in rodents outside of the Arvicolinae or from localities in the Nearctic. These studies emphasize the need for routine deposition of archival specimens and information, from survey, ecological, and biogeographic studies, in museum collections to serve as self-correcting records for biodiversity at local, regional, and continental scales.

Ticks feeding on northern pocket gophers (Thomomys talpoides) in central Saskatchewan and the unexpected detection of Ixodes scapularis larvae.

Morphological examination of ticks feeding on northern pocket gophers, Thomomys talpoides, near Clavet (Saskatchewan, Canada) revealed the presence of two genera, Ixodes and Dermacentor. All adult ticks collected were identified as I. kingi. Single strand conformation polymorphism (SSCP) analyses and DNA sequencing of the mitochondrial 16S rRNA gene confirmed the species identity of most Ixodes immatures as I. kingi (two nymphs and 82 larvae), and the Dermacentor immatures as D. variabilis (one nymph and one larva) and D. andersoni (three larvae). Six Ixodes larvae feeding on three T. talpoides individuals were identified as four different 16S haplotypes of I. scapularis, which was unexpected because there are no known established populations of this species in Saskatchewan. However, flagging for questing ticks and further examination of the ticks feeding on T. talpoides in two subsequent years failed to detect the presence of I. scapularis near Clavet, suggesting that there is no established population of I. scapularis in this area. Nonetheless, since I. scapularis is a vector of pathogenic agents, passive and active surveillance needs to be conducted in Saskatchewan on an ongoing basis to determine if this tick species and its associated pathogens become established within the province.

Molecular systematics of the Holarctic Anoplocephaloides variabilis (Douthitt, 1915) complex, with the proposal of Microcephaloides n. g. (Cestoda: Anoplocephalidae).

Phylograms based on mitochondrial cytochrome oxidase I gene sequences show that the Anoplocephaloides variabilis (Douthitt, 1915)-like cestodes (Cestoda: Anoplocephalidae) from voles (Microtus spp.) and Paranoplocephala krebsi Haukisalmi, Wickström, Hantula & Henttonen, 2001 from collared lemmings (Dicrostonyx spp.) comprise a monophyletic group within the anoplocephaline cestodes. The patterns of phylogenetic, biological and/or biogeographical distinction suggest six or seven species of A. variabilis-like cestodes, including P. krebsi. However, at this time we decline to describe them as a series of new species as no straightforward morphological differences were found between the A. variabilis-like cestodes. A new genus, Microcephaloides n. g., is proposed for the cestodes earlier assigned to A. variabilis, A. cf. variabilis, A. tenoramuraiae Genov & Georgiev, 1988 and P. krebsi. A redescription is provided for the type-species, M. variabilis n. comb., from pocket gophers (Geomys spp. and Thomomys spp.). In addition to Anoplocephaloides Baer, 1927 (sensu stricto) and Microcephaloides, Paranoplocephaloides Gulyaev, 1996, Flabelloskrjabinia Spasskii, 1951 and Leporidotaenia Genov, Murai, Georgiev & Harris, 1990 are considered valid genera among cestodes previously assigned to Anoplocephaloides (sensu Rausch, 1976). The host spectrum and present phylogenetic data suggest that Microcephaloides has been primarily associated with voles (Microtus spp.) and its basal lineage now occurs in M. guentheri (Danford & Alston) in Turkey. Although the distribution and current host of the basal lineage suggest a western Palaearctic origin, subsequent diversification has probably occurred in eastern Beringia, because most of the more derived lineages occur partly or exclusively in Alaska.

A new species of Vexillata (Nematoda: Ornithostrongylidae) in Attwater's pocket gopher from Texas.

Vexillata geomyos n. sp. is described as a parasite of Attwater's pocket gopher, Geomys attwateri (Geomyidae), from Welder Wildlife Refuge, Texas. The new species possesses 12 cuticular ridges; based on this character, it can be distinguished from 7 of the 13 species in the genus. From the 6 remaining species, V. geomyos can be differentiated because the dorsal ray in 3 of them (V. armandae, V. dessetae, and V. vexillata) has 2 short branches arising from main trunk, whereas dorsal ray of the new species lacks these branches. In addition, V. geomyos can be distinguished from V. brooksi because its spicules are divided at the tip (whereas in the new species, spicules are whole). The new species differs from V. legallae and V. convoluta in the number and arrangement of cuticular ridges at the posterior region of the body.

Systematic position of some nearctic Heligmosomoidea (Nematoda: Trichostrongylina) from the U.S. National Parasite collection and their description.

The systematic position of some heligmosomoid nematodes from rodents, deposited in the U.S. National Parasite Collection (USNPC), is revised, mainly through the study of their synlophe, which in all cases was unknown or insufficiently described. The material was registered as different species of Longistriata Schulz, 1926, a genus whose representatives are only parasitic in Holarctic insectivores. Longistriata norvegica Dikmans, 1935, parasitic in Rattus sp. becomes a synonym of Hassalstrongylus aduncus (Chandler, 1932). Specimens registered as Longistriata dalrymplei Dikmans, 1935, from Ondatra zibethicus, are confirmed to belong to Carolinensis (Travassos, 1937). Specimens registered as Longistriata noviberiae Dikmans, 1935, parasitic in Sylvilagus floridanus alacer, were found to belong to Vexillata, and Vexillata noviberiae n. comb. is here proposed. This is the first record of a species of Vexillata in a lagomorph. Other specimens registered as Longistriata norvegica, parasitic in Geomys floridanus austrinus, were also found to be an undescribed species of Vexillata (Hall, 1916), which is named Vexillata chitwoodi n. sp. This is similar to Vexillata chabaudi Yoyotte-Vado, 1972, Vexillata petteri Durette-Desset, 1970, Vexillata scorzai Guerrero, 1984 and Vexillata tejerai Guerrero, 1984, all having the same number of cuticular ridges (4 dorsal, 5 ventral) and the division of the dorsal ray at its apex. The most related species is V. chabaudi, which is differentiated from the new species by rays 4 not curved distally, by thick rays 8, and by a dorsal ray enlarged at the level of the arising of rays 8.