Development of eighteen novel microsatellite loci for Masked Bobwhite, Colinus virginianus ridgwayi.

BACKGROUND: Masked Bobwhite (Colinus virginianus ridgwayi) is a critically-endangered New World quail species endemic to Sonoran Desert grasslands of North America. It suffered severe population declines during the nineteenth and twentieth centuries, with its persistence now reliant upon a captive breeding program that requires careful genetic management to maintain extant genetic diversity. Although nuclear microsatellite DNA markers existed for the closely related Northern Bobwhite (C. virginianus), none were available for Masked Bobwhite to inform necessary management decisions. METHODS AND RESULTS: Paired-end Illumina© sequencing was conducted to screen the Masked Bobwhite genome for microsatellite loci. We identified 18 loci exhibiting high polymorphism and limited deviations from genetic equilibrium expectations. These loci were amplified in 78 individuals. Familial relationships were reconstructed via sibship methods and compared to manually-curated pedigree data. Thirteen of fifteen full-sibling groups in the pedigree were exactly reconstructed (86.6%). Three other full-sibling groups partially matched pedigree relationships with high statistical confidence, and likely represented pedigree inaccuracies. Four additional full-sibling pairs were identified with low statistical confidence and likely resulted from analytical artifacts. CONCLUSIONS: The novel microsatellite loci accurately reconstructed parent-offspring and sibling relationships. These loci will be useful for guiding genetic management decisions and identifying pedigree inaccuracies in the captive breeding program.

Development of twenty-one novel microsatellite loci for Gila topminnow, Poeciliopsis occidentalis occidentalis.

BACKGROUND: Gila topminnow (Poeciliopsis occidentalis occidentalis) was once highly abundant throughout the Lower Colorado River Basin of the southwestern United States. However, this Sonoran Desert endemic suffered extreme population declines over the past century because of habitat degradation and nonnative species introductions. Much of the prior conservation genetic work conducted on the species relied upon a small number of microsatellite loci; many exhibiting low variability in extant populations. Consequently, there was a need for additional microsatellite loci to provide high-resolution delimitation of populations for conservation purposes. METHODS AND RESULTS: Paired-end Illumina sequencing was utilized to screen the Gila topminnow genome for novel microsatellite loci. We identified 21 novel loci that exhibited no deviations from expectations of genetic equilibrium, and cross-amplified in Yaqui topminnow (P. o. sonoriensis). These loci were amplified from 401 samples representing eight populations of Gila topminnow and Yaqui topminnow. Although diversity was low for all populations (observed heterozygosity = 0.12 to 0.45), these novel markers provided ample power to identify population of origin for each individual in Bayesian assignment tests. CONCLUSIONS: This novel set of microsatellite loci provide a useful genetic tool to assess population genetic parameters of the endangered Gila topminnow and delineate populations for identifying conservation priorities. The cross-amplification of these loci in Yaqui topminnow shows promise for application to other Poeciliopsis species of Mexico and Central America.

Phylogenetic analysis of the Pacific cutthroat trout (Oncorhynchus clarki ssp.: Salmonidae) based on partial mtDNA ND4 sequences: a closer look at the highly fragmented inland species.

The genus Oncorhynchus includes Pacific salmon and trout (anadromous and land-locked) species of the western United States and Mexico. All species and subspecies in this group are threatened, endangered, sensitive, or species of conservation concern in portions of their native ranges. To examine the relationships of the species within Oncorhynchus we sequenced a 768 bp fragment of the protein-encoding ND4 mtDNA region. We included all six recognized subspecies of O. clarki (cutthroat trout), O. gilaegilae (Gila trout) and O. g. apache (Apache trout). Gene trees from likelihood and Bayesian phylogenetic analyses revealed that Salvelinus was the sister group to Oncorhynchus, and as expected based on previous studies, O. clarki was sister to a clade that consisted of O. mykiss plus O. g. gilae and O. g. apache. Within the cutthroat clade (O. clarki), the coastal form O. c. clarki was basal with the Rio Grande cutthroat (O. c. virginalis) most derived. Divergence dating based on a fossil calibration molecular clock showed the oldest clade (mean node age) was O. masou ssp., which diverged roughly 7.6 MYA. Highest probability density intervals for divergence of O. masou overlapped with divergence (6.3 MYA) of Pacific salmon clades ((O. gorbuscha + O. nerka) and (O. tshawytscha + O. kisutch)). The Pacific trout clade ((O. mykiss + O. gilae ssp.) + (O. clarki ssp.)) diverged from the Pacific salmon around 6.3 MYA, with most of the diversification within the O. clarki clade occurring in the last 1 MY.

Introgressive hybridization of human and rodent schistosome parasites in western Kenya.

Hybridization and introgression can have important consequences for the evolution, ecology and epidemiology of pathogenic organisms. We examined the dynamics of hybridization between a trematode parasite of humans, Schistosoma mansoni, and its sister species, S. rodhaini, a rodent parasite, in a natural hybrid zone in western Kenya. Using microsatellite markers, rDNA and mtDNA, we showed that hybrids between the two species occur in nature, are fertile and produce viable offspring through backcrosses with S. mansoni. Averaged across collection sites, individuals of hybrid ancestry comprised 7.2% of all schistosomes collected, which is a large proportion given that one of the parental species, S. rodhaini, comprised only 9.1% of the specimens. No F1 individuals were collected and all hybrids represented backcrosses with S. mansoni that were of the first or successive generations. The direction of introgression appears highly asymmetric, causing unidirectional gene flow from the rodent parasite, S. rodhaini, to the human parasite, S. mansoni. Hybrid occurrence was seasonal and most hybrids were collected during the month of September over a 2-year period, a time when S. rodhaini was also abundant. We also examined the sex ratios and phenotypic differences between the hybrids and parental species, including the number of infective stages produced in the snail host and the time of day the infective stages emerge. No statistical differences were found in any of these characteristics, and most of the hybrids showed an emergence pattern similar to that of S. mansoni. One individual, however, showed a bimodal emergence pattern that was characteristic of both parental species. In conclusion, these species maintain their identity despite hybridization, although introgression may cause important alterations of the biology and epidemiology of schistosomiasis in this region.

A molecular phylogenetic study of the genus Ribeiroia (Digenea): trematodes known to cause limb malformations in amphibians.

Species of Ribeiroia (Trematoda: Psilostomidae) are known to cause severe limb malformations and elevated mortality in amphibians. However, little is known regarding the number of species in this genus or its relation to other taxa. Species of Ribeiroia have historically been differentiated by slight differences among their larval stages. To better understand the systematics and biogeography of this genus and their potential relevance to the distribution of malformed amphibians, specimens identified as Ribeiroia were collected across much of the known range, including samples from 5 states in the United States (8 sites) and 2 islands in the Caribbean (Puerto Rico and Guadeloupe). A cercaria from East Africa identified as Cercaria lileta (Fain, 1953), with attributes suggestive of Ribeiroia (possibly R. congolensis), was also examined. The intertranscribed spacer region 2 (ITS-2) of the ribosomal gene complex was sequenced and found to consist of 429 nucleotides (nt) for R. ondatrae (United States) and 427 nt for R. marini (Caribbean), with only 6 base differences noted between the 2 species. The ITS-2 region of C. lileta (429 nt) aligned closely with those of the 2 other Ribeiroia species in a phylogenetic analysis that included related trematode genera. This evidence suggests that a third Ribeiroia species exists in tropical Africa. Variation in ITS-2 within R. ondatrae was nonexistent among the 8 populations from North America. Our study further suggests that Ribeiroia spp. originally parasitized Biomphalaria sp., and that a host switch to a closely related snail, Helisoma sp., may have occurred in the lineage represented by R. ondatrae. However, relationships within the Echinostomatidae are not understood well enough to make any robust conclusions at this time.