Thousands of induced germline mutations affecting immune cells identified by automated meiotic mapping coupled with machine learning.

Forward genetic studies use meiotic mapping to adduce evidence that a particular mutation, normally induced by a germline mutagen, is causative of a particular phenotype. Particularly in small pedigrees, cosegregation of multiple mutations, occasional unawareness of mutations, and paucity of homozygotes may lead to erroneous declarations of cause and effect. We sought to improve the identification of mutations causing immune phenotypes in mice by creating Candidate Explorer (CE), a machine-learning software program that integrates 67 features of genetic mapping data into a single numeric score, mathematically convertible to the probability of verification of any putative mutation-phenotype association. At this time, CE has evaluated putative mutation-phenotype associations arising from screening damaging mutations in ∼55% of mouse genes for effects on flow cytometry measurements of immune cells in the blood. CE has therefore identified more than half of genes within which mutations can be causative of flow cytometric phenovariation in Mus musculus The majority of these genes were not previously known to support immune function or homeostasis. Mouse geneticists will find CE data informative in identifying causative mutations within quantitative trait loci, while clinical geneticists may use CE to help connect causative variants with rare heritable diseases of immunity, even in the absence of linkage information. CE displays integrated mutation, phenotype, and linkage data, and is freely available for query online.

Recognizing the Causes of Parasite Morphological Variation to Resolve the Status of a Cryptogenic Pentastome.

Exotic species can threaten biodiversity by introducing parasites to native hosts. Thus, it is critical to identify if the same parasite species infects both native and exotic hosts. However, developmental- or environmental-induced morphological variation may render species identification ambiguous. Our study reports a range expansion in the southern United States of the pentastome Raillietiella indica from the Mediterranean gecko, Hemidactylus turcicus, as well as a host expansion into the green anole, Anolis carolinensis, in the anole's native range. Species identification was based on sequence data and male spicule shape. In agreement with a study from Australia, we found that much of the morphological variation in hook measurements, the primary diagnostic traits of raillietiellid pentastomes, was due to development. Here, we explicitly link this developmental variation to instar stage by incorporating experimental infection data obtained from the literature. We also show that the various hook traits are themselves highly correlated and, thus, likely not independent. Taking instar stage and correlated hook variables into account, we directly controlled for development on a composite hook size measurement. Using a large sample size from H. turcicus, we did not find any consistent effects of potential factors (host sex, host snout-vent-length, or parasite intensity) that may result in environmental-induced variation in relative hook size (corrected for body length). However, relative male spicule size tended to be negatively correlated with parasite intensity. In contrast, both pentastome body length and relative hook size significantly varied among host species whereas relative male spicule size was not significantly different among host species. Our study independently supports the conclusions that developmental- and host-induced morphological variations need to be accounted for to accurately identify pentastome species.

Physiological Status Drives Metabolic Rate in Mediterranean Geckos Infected with Pentastomes.

Negative effects of parasites on their hosts are well documented, but the proximate mechanisms by which parasites reduce their host's fitness are poorly understood. For example, it has been suggested that parasites might be energetically demanding. However, a recent meta-analysis suggests that they have statistically insignificant effects on host resting metabolic rate (RMR). It is possible, though, that energetic costs associated with parasites are only manifested during and/or following periods of activity. Here, we measured CO2 production (a surrogate for metabolism) in Mediterranean geckos (Hemidactylus turcicus) infected with a lung parasite, the pentastome Raillietiella indica, under two physiological conditions: rested and recently active. In rested geckos, there was a negative, but non-significant association between the number of pentastomes (i.e., infection intensity) and CO2 production. In recently active geckos (chased for 3 minutes), we recorded CO2 production from its maximum value until it declined to a stationary phase. We analyzed this decline as a 3 phase function (initial decline, secondary decline, stationary). Geckos that were recently active showed, in the secondary phase, a significant decrease in CO2 production as pentastome intensity increased. Moreover, duration of the secondary phase showed a significant positive association with the number of pentastomes. These results suggest that the intensity of pentastome load exerts a weak effect on the metabolism of resting geckos, but a strong physiological effect on geckos that have recently been active; we speculate this occurs via mechanical constraints on breathing. Our results provide a potential mechanism by which pentastomes can reduce gecko fitness.