Affordable sequencing and genotyping methods are essential for large-scale genome-wide association studies. While genotyping microarrays and reference panels for imputation are available for human subjects, nonhuman model systems often lack such options. Our lab previously demonstrated an efficient and cost-effective method to genotype heterogeneous stock rats using double-digest genotyping by sequencing. However, low-coverage whole-genome sequencing offers an alternative method that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy genotyping method for N/NIH heterogeneous stock rats that can use a combination of sequencing data previously generated by double-digest genotyping by sequencing and more recently generated by low-coverage whole-genome sequencing data. Using double-digest genotyping-by-sequencing data from 5,745 heterogeneous stock rats (mean 0.21× coverage) and low-coverage whole-genome sequencing data from 8,760 heterogeneous stock rats (mean 0.27× coverage), we can impute 7.32 million biallelic single-nucleotide polymorphisms with a concordance rate > 99.76% compared to high-coverage (mean 33.26× coverage) whole-genome sequencing data for a subset of the same individuals. Our results demonstrate the feasibility of using sequencing data from double-digest genotyping by sequencing or low-coverage whole-genome sequencing for accurate genotyping and demonstrate techniques that may also be useful for other genetic studies in nonhuman subjects.

Species-specific sexual traits facilitate species-assortative mating by reducing mating across species and reducing hybrid sexual attractiveness. For learned sexual traits, such as song in oscine birds, species distinctiveness can be eroded when species co-occur. Transcriptional regulatory divergence in brain regions involved in sensory learning is hypothesized to maintain species distinctiveness, but relatively few studies have compared gene expression in relevant brain regions between closely related species. Species differences in song are an important premating reproductive barrier between the collared (Ficedula albicollis) and pied flycatcher (F. hypoleuca). Here, we compare brain gene expression in adult males from each species and their naturally occurring F1 hybrids. We report overall conserved expression across species in a portion of the brain containing regions and nuclei known to be involved in song responses and learning. Further, among those genes that were differentially expressed between species, we find largely intermediate expression in hybrids. A single gene, SYT4 (synaptotagmin 4), known to be singing-associated, both was differentially expressed and has a putative upstream transcriptional regulatory factor containing fixed differences between the 2 species. Although a finer-scale investigation limited to song-specific regions may reveal further species differences, our findings provide insight into regulatory divergence in the brain between closely related species.

Tetrapedia diversipes is a Neotropical solitary bee commonly found in trap-nests, known for its morphological adaptations for floral oil collection and prepupal diapause during the cold and dry season. Here, we present the genome assembly of T. diversipes (332 Mbp), comprising 2,575 scaffolds, with 15,028 predicted protein-coding genes. Repetitive elements constitute 38.68% of the genome, notably Class II transposable elements. An investigation into lateral gene transfers identified a low frequency (0.037%) of nuclear copies of mitochondrial DNA and 18 candidate regions from bacterial origins. Furthermore, the annotation of 3 scaffolds reveals the presence of the Wolbachia endosymbiont genome, confirming the infection by 2 strains in T. diversipes populations. This genome contributes valuable insights into Neotropical bee genomics, offering a resource for comparative studies and enhancing our understanding of the molecular basis of solitary bee adaptations and interactions.

This study presents a frequency-specific, pedigree-based assessment of hearing acuity heritability. We analysed 34 Utah Centre d'Etude du Polymorphisme Humain (CEPH) pedigrees comprising 464 individuals, using whole-genome sequencing (WGS) and audiometric evaluations. Our analysis reveals a general decline in narrow-sense heritability as frequency increases. When calculated using the Sequential Oligogenic Linkage Analysis Routines (SOLAR) software package, narrow-sense heritability estimates drop from 51% at 250 Hz to 30% at 8000 Hz. Genetic correlations (Rho(G)), the degree to which genetic variation in one trait correlates with another, are higher for hearing acuity at similar frequencies. For example, Rho(G) between 250 and 500 Hz is 0.80, and Rho(G) between 6000 and 8000 Hz is 0.91. In contrast, frequencies distant from each other exhibit decreased Rho(G) with a genetic correlation of only 0.21 for hearing acuity at frequencies 250 and 8000 Hz. This assessment of the genetics underlying hearing acuity in a family-based design provides new details of genetic factors influencing hearing acuity in a frequency-specific approach.

The soybean tentiform leafminer, Macrosaccus morrisella (Fitch) (Lepidoptera: Gracillariidae), is native to North America where it was known to feed on American hogpeanut and slickseed fuzzybean. However, it has recently expanded its host range to include soybean, an important agricultural crop. Here we report a new, highly contiguous genome for this species with a length of 245 Mb, N50 of 9 Mb, and 96.33% BUSCO completeness. The mitochondrial genome shares only 81% identity to its nearest relative in the NCBI nucleotide database indicating long-standing divergence or sparse sequencing in this clade. To determine whether host plant choice is genetically driven, we sequenced 18 individuals across three locations in Minnesota, United States, collected from both American hogpeanut and soybean plants. Genetic variation did not correlate with population structure based on either geography or host plant species (weighted FST estimate: 0.0058). As a secondary measure, we independently assembled complete mitochondrial genomes from all individuals and observed no delineation between host or location. Overall lack of detectable population structure at the nuclear and mitochondrial genome levels suggests a large population with flexible dietary preferences and does not show evidence of genetically driven host preference.

Coral populations worldwide are declining rapidly due to elevated ocean temperatures and other human impacts. The Caribbean harbors a high number of threatened, endangered, and critically endangered coral species compared to reefs of the larger Indo-Pacific. The reef corals of the Caribbean are also long diverged from their Pacific counterparts and may have evolved different survival strategies. Most genomic resources have been developed for Pacific coral species which may impede our ability to study the changes in genetic composition of Caribbean reef communities in response to global change. To help fill the gap in genomic resources, we used PacBio HiFi sequencing to generate the first genome assemblies for three Caribbean, reef-building corals, Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea. We also explore the genomic novelties that shape scleractinian genomes. Notably, we find abundant gene duplications of all classes (e.g., tandem and segmental), especially in S. siderea. This species has one of the largest genomes of any scleractinian coral (822Mb) which seems to be driven by repetitive content and gene family expansion and diversification. As the genome size of S. siderea was double the size expected of stony corals, we also evaluated the possibility of an ancient whole genome duplication using Ks tests and found no evidence of such an event in the species. By presenting these genome assemblies, we hope to develop a better understanding of coral evolution as a whole and to enable researchers to further investigate the population genetics and diversity of these three species.

The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.

Genetic studies of Plasmodium parasites increasingly feature relatedness estimates. However, various aspects of malaria parasite relatedness estimation are not fully understood. For example, relatedness estimates based on whole-genome-sequence (WGS) data often exceed those based on sparser data types. Systematic bias in relatedness estimation is well documented in the literature geared towards diploid organisms, but largely unknown within the malaria community. We characterise systematic bias in malaria parasite relatedness estimation using three complementary approaches: theoretically, under a non-ancestral statistical model of pairwise relatedness; numerically, under a simulation model of ancestry; and empirically, using data on parasites sampled from Guyana and Colombia. We show that allele frequency estimates encode, locus-by-locus, relatedness averaged over the set of sampled parasites used to compute them. Plugging sample allele frequencies into models of pairwise relatedness can lead to systematic underestimation. However, systematic underestimation can be viewed as population-relatedness calibration, i.e., a way of generating measures of relative relatedness. Systematic underestimation is unavoidable when relatedness is estimated assuming independence between genetic markers. It is mitigated when relatedness is estimated using WGS data under a hidden Markov model (HMM) that exploits linkage between proximal markers. The extent of mitigation is unknowable when a HMM is fit to sparser data, but downstream analyses that use high relatedness thresholds are relatively robust regardless. In summary, practitioners can either resolve to use relative relatedness estimated under independence, or try to estimate absolute relatedness under a HMM. We propose various tools to help practitioners evaluate their situation on a case-by-case basis.

Retinopathy with Vitamin E Deficiency (RVED) is a familial disease in the English Cocker Spaniel (ECS) dog breed. Ophthalmic abnormalities observed in RVED-affected ECS include lipofuscin granule deposition within the tapetal fundus and subsequent retinal degeneration resulting in visual deficits. Affected dogs may also exhibit neurological signs that include ataxia and hindlimb proprioceptive deficit. In all cases, circulating plasma concentrations of α-tocopherol are low. This study sought to investigate the genetic basis of RVED in the ECS breed. We undertook a genome-wide association study comprising 30 ECS with normal fundic examinations aged 6 years or older (controls) and 20 diagnosed with RVED (cases) and identified a statistically associated signal on chromosome 29 (Praw = 1.909×10-17). Whole genome sequencing (WGS) of two cases identified a 102bp deletion in exon 1 of the Alpha Tocopherol Transfer Protein gene (TTPA), truncating the protein by 34 amino acids. The c.23_124del variant segregated with RVED in a total of 30 cases and 43 controls. Variants in TTPA are causal for Ataxia with Vitamin E Deficiency (AVED) in humans which is a phenotypically similar disease to RVED. The identification of the canine variant is extremely significant as the availability of a DNA test will allow for identification of presymptomatic dogs and early therapeutic intervention which may prevent development of retinopathy and improve neurological signs. Breeders can also use the DNA test to efficiently eradicate the disease from this breed.

Atahualpa is a rural village located in coastal Ecuador, a region that has been inhabited by people as early as 10,000 years ago. The traditional diet of their indigenous inhabitants is rich in oily fish and they have, therefore, served as a model for investigating the beneficial effects of such a diet. However, the genetic background of this population has not been studied. In this study, we sequenced the genomes of Atahualpa residents to look for variants under natural selection, which could mediate the effects of oily fish intake. DNA was extracted from 50 blood samples from randomly selected individuals recruited in the Atahualpa Project Cohort. After applying various filters, we calculated genome-wide genotype likelihoods from 33 samples, and combined data from those samples with data from other populations to investigate how the Atahualpa population is genetically related to these populations. Using selection scans, we identified signals of natural selection that may explain the above-mentioned dietary effects. The genetic ancestry in Atahualpa residents is 94.1% of indigenous American origin, but is substantially diverged from other indigenous populations in neighboring countries. Significant signatures of natural selection were found in the Atahualpa population, including a broad selection signal around the SUFU gene, which is a repressor of Hedgehog pathway signaling and associated with lipid metabolism, and another signal in the upstream region of LRP1B which encodes low-density lipoprotein (LDL) receptor related protein 1B. Our selection study reveals genes under selection in the Atahualpa population, which could mediate the beneficial effects of oily fish intake in this population.