Thermal sensitivity and seasonal change in the gut microbiome of a desert ant, Cephalotes rohweri

Microorganisms within ectotherms must withstand the variable body temperatures of their hosts. Shifts in host body temperature resulting from climate change have the potential to shape ectotherm microbiome composition. Microbiome compositional changes occurring in response to temperature in nature have not been frequently examined, restricting our ability to predict microbe-mediated ectotherm responses to climate change. In a set of field-based observations, we characterized gut bacterial communities and thermal exposure across a population of desert arboreal ants (Cephalotes rohweri). In a paired growth chamber experiment, we exposed ant colonies to variable temperature regimes differing by 5 °C for three months. We found that the abundance and composition of ant-associated bacteria were sensitive to elevated temperatures in both field and laboratory experiments. We observed a subset of taxa that responded similarly to temperature in the experimental and observational study, suggesting a role of seasonal temperature and local temperature differences amongst nests in shaping microbiomes within the ant population. Bacterial mutualists in the genus Cephaloticoccus (Opitutales: Opitutaceae) were especially sensitive to change in temperature-decreasing in abundance in naturally warm summer nests and warm growth chambers. We also report the discovery of a member of the Candidate Phlya Radiation (Phylum: Gracilibacteria), a suspected epibiont, found in low abundance within the guts of this ant species.

Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci

The search for quantitative trait loci that explain complex traits such as yield and drought tolerance has been ongoing in all crops. Methods such as biparental quantitative trait loci mapping and genome-wide association studies each have their own advantages and limitations. Multiparent advanced generation intercross populations contain more recombination events and genetic diversity than biparental mapping populations and are better able to estimate effect sizes of rare alleles than association mapping populations. Here, we discuss the results of using a multiparent advanced generation intercross population of doubled haploid maize lines created from 16 diverse founders to perform quantitative trait loci mapping. We compare 3 models that assume bi-allelic, founder, and ancestral haplotype allelic states for quantitative trait loci. The 3 methods have differing power to detect quantitative trait loci for a variety of agronomic traits. Although the founder approach finds the most quantitative trait loci, all methods are able to find unique quantitative trait loci, suggesting that each model has advantages for traits with different genetic architectures. A closer look at a well-characterized flowering time quantitative trait loci, qDTA8, which contains vgt1, highlights the strengths and weaknesses of each method and suggests a potential epistatic interaction. Overall, our results reinforce the importance of considering different approaches to analyzing genotypic datasets, and shows the limitations of binary SNP data for identifying multiallelic quantitative trait loci.

Analysis of genotype-by-environment interactions in a maize mapping population

Genotype-by-environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype-by-environment interactions in a maize multiparent advanced generation intercross population grown across 5 environments. We found that genotype-by-environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. To understand how genetic correlations between traits change across environments, we estimated the genetic variance–covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype-by-environment variance. We also performed a genome-wide association study to identify markers associated with genotype-by-environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype-by-environment interactions in this population.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

Genotype-by-genotype interactions between an insect and its pathogen

Genotype-by-genotype (G×G) interactions are an essential requirement for the coevolution of hosts and parasites, but have only been documented in a small number of animal model systems. G×G effects arise from interactions between host and pathogen genotypes, such that some pathogen strains are more infectious in certain hosts and some hosts are more susceptible to certain pathogen strains. We tested for G×G interactions in the gypsy moth (Lymantria dispar) and its baculovirus. We infected 21 full-sib families of gypsy moths with each of 16 isolates of baculovirus and measured the between-isolate correlations of infection rate across host families for all pairwise combinations of isolates. Mean infectiousness varied among isolates and disease susceptibility varied among host families. Between-isolate correlations of infection rate were generally less than one, indicating nonadditive effects of host and pathogen type consistent with G×G interactions. Our results support the presence of G×G effects in the gypsy moth-baculovirus interaction and provide empirical evidence that correlations in infection rates between field-collected isolates are consistent with values that mathematical models have previously shown to increase the likelihood of pathogen polymorphism.

Fundamental frequency characteristics of young Black adults: spontaneous speaking and oral reading

The purpose of this study was to determine the speaking fundamental vocal frequency of young Black adults during prompted spontaneous speech and reading and to compare the results with published data for White subjects of comparable age. Subjects were 100 men and 100 women volunteers, ranging in age from 18 to 29 years. Central tendency and dispersion values were calculated from data obtained with a fundamental frequency analyzer (Florida I). The mean modal fundamental vocal frequency for spontaneous speaking was 108.05 Hz for men and 188.85 Hz for women. The mean range was 80.70--166.65 Hz (6.27 tones) for men and 132.55--270.80 Hz (6.18 tones) for women. The men showed smaller excursions from the mean mode to the lower limit of the mean range (27.35 hz, 2.52 tones) than from the mean mode to the upper limit of the mean range (58.60 Hz, 3.75 tones). The women had a range of 81.95 Hz above and 56.30 Hz below the mean mode but approximately equal tonal intervals above and below (3.12 and 3.06, respectively). A comparison of prompted spontaneous speech to reading for the same subjects indicated that the mean modal fundamental vocal frequency was significantly lower and the mean range was significantly greater for speaking than for reading. Both men and women had a mean speaking range of one octave. In comparison to published values for young White adult subjects, the Black subjects in this study had a lower mean fundamental vocal frequency.

A study of the reading fundamental vocal frequency of young black adults

This study investigated the measures of central tendency (mean mode) and dispersion (standard deviations and ranges) of the reading fundamental vocal frequency in young black adults. The subjects were 200 (100 males/100 females) college student volunteers whose ages ranged from 18 to 29 years. A fundamental frequency analyzer (FLORIDA I) was used to measure the fundamental vocal frequency. The mean modal fundamental vocal frequency for males was 110.15 Hz, with a mean range from 81.95 Hz to 158.50 Hz. The mean modal fundamental vocal frequency for females was 193.10 Hz, with a mean range from 139.05 Hz to 266.10 Hz. The males showed a slightly greater range expressed in tones than did the females. Compared to a similar white population studied by Fitch & Holbrook (1970), the black population had lower mean modal fundamental vocal frequencies and greater mean frequency ranges. Fitch's white subjects showed a greater range below the mean mode than above it. This behavior was reversed for the black subjects of the present study. Such patterns of vocal behavior may be important clues which alert the listener to the speaker's racial identity.