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Most organisms are more closely related to nearby than distant members of their species, creating spatial autocorrelations in genetic data. This allows us to predict the location of origin of a genetic sample by comparing it to a set of samples of known geographic origin. Here, we describe a deep learning method, which we call Locator, to accomplish this task faster and more accurately than existing approaches. In simulations, Locator infers sample location to within 4.1 generations of dispersal and runs at least an order of magnitude faster than a recent model-based approach. We leverage Locator’s computational efficiency to predict locations separately in windows across the genome, which allows us to both quantify uncertainty and describe the mosaic ancestry and patterns of geographic mixing that characterize many populations. Applied to whole-genome sequence data from Plasmodium parasites, Anopheles mosquitoes, and global human populations, this approach yields median test errors of 16.9km, 5.7km, and 85km, respectively.

During range expansions, species can experience rapid population growth if changes in climate or interspecific interactions remove limits on growth rates in novel habitats. Here I document a century of range expansion in the Anna's hummingbird (Calypte anna) and investigate the causes of its recent abundance through a combination of demographic, climatic, and phenological analyses. Christmas Bird Count records indicate that populations have been growing in California since the early twentieth century. Sites across the Pacific Northwest show striking fits to simple models of exponential growth following colonization in the 1960s and 1970s, and nest records indicate that the species now delays the start of the nesting season by at least 16 days in the north. Although the species now occurs in a much wider range of climates than before the range expansion, the fastest growing populations in the northwest are in regions with minimum breeding season temperatures similar to those occupied by the species in its native range. Range expansions in the Anna's hummingbird thus reflect an ecological release likely caused by a mix of introduced plants, human facilitation, and phenological acclimation that allowed a California native to expand across western North America.

Dimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMAP). Here we explore the utility of variational autoencoders (VAEs)—generative machine learning models in which a pair of neural networks seek to first compress and then recreate the input data—for visualizing population genetic variation. VAEs incorporate nonlinear relationships, allow users to define the dimensionality of the latent space, and in our tests preserve global geometry better than t-SNE and UMAP. Our implementation, which we call popvae, is available as a command-line python program at github.com/kr-colab/popvae. The approach yields latent embeddings that capture subtle aspects of population structure in humans and Anopheles mosquitoes, and can generate artificial genotypes characteristic of a given sample or population.

Background We have previously shown that the expression of a constitutively active nitrate reductase variant and the suppression of CLCNt2 gene function (belonging to the chloride channel (CLC) gene family) in field-grown tobacco reduces tobacco-specific nitrosamines (TSNA) accumulation in cured leaves and cigarette smoke. In both cases, TSNA reductions resulted from a strong diminution of free nitrate in the leaf, as nitrate is a precursor of the TSNA-producing nitrosating agents formed during tobacco curing and smoking. These nitrosating agents modify tobacco alkaloids to produce TSNAs, the most problematic of which are NNN (N-nitrosonornicotine) and NNK (4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone). The expression of a deregulated nitrate reductase enzyme (DNR) that is no longer responsive to light regulation is believed to diminish free nitrate pools by immediately channeling incoming nitrate into the nitrate assimilation pathway. The reduction in nitrate observed when the two tobacco gene copies encoding the vacuolar nitrate transporter CLCNt2 were down-regulated by RNAi-mediated suppression or knocked out using the CRISPR-Cas technology was mechanistically distinct; likely attributable to the inability of the tobacco cell to efficiently sequester nitrate into the vacuole where this metabolite is protected from further assimilation. In this study, we used transcriptomic and metabolomic analyses to compare the nitrate assimilation response in tobacco plants either expressing DNR or lacking CLCNt2 function. Results When grown in a controlled environment, both DNR and CLCNt2-KO (CLCKO) plants exhibited (1) reduced nitrate content in the leaf; (2) increased N-assimilation into the amino acids Gln and Asn; and (3) a similar pattern of differential regulation of several genes controlling stress responses, including water stress, and cell wall metabolism in comparison to wild-type plants. Differences in gene regulation were also observed between DNR and CLCKO plants, including genes encoding nitrite reductase and asparagine synthetase. Conclusions Our data suggest that even though both DNR and CLCKO plants display common characteristics with respect to nitrate assimilation, cellular responses, water stress, and cell wall remodeling, notable differences in gene regulatory patterns between the two low nitrate plants are also observed. These findings open new avenues in using plants fixing more nitrogen into amino acids for plant improvement or nutrition perspectives.

Background Nicotiana rustica (Aztec tobacco), like common tobacco ( Nicotiana tabacum ), is an allotetraploid formed through a recent hybridization event; however, it originated from completely different progenitor species. Here, we report the comparative genome analysis of wild type N. rustica (5 Gb; 2n = 4x = 48) with its three putative diploid progenitors (2.3–3 Gb; 2n = 2x =24), Nicotiana undulata , Nicotiana paniculata and Nicotiana knightiana . Results In total, 41% of N. rustica genome originated from the paternal donor ( N. undulata ), while 59% originated from the maternal donor ( N. paniculata / N. knightiana ). Chloroplast genome and gene analyses indicated that N. knightiana is more closely related to N. rustica than N. paniculata . Gene clustering revealed 14,623 ortholog groups common to other Nicotiana species and 207 unique to N. rustica . Genome sequence analysis indicated that N. knightiana is more closely related to N. rustica than N. paniculata , and that the higher nicotine content of N. rustica leaves is the result of the progenitor genomes combination and of a more active transport of nicotine to the shoot. Conclusions The availability of four new Nicotiana genome sequences provide insights into how speciation impacts plant metabolism, and in particular alkaloid transport and accumulation, and will contribute to better understanding the evolution of Nicotiana species.

Levels of genetic differentiation vary widely along the genomes of recently diverged species. What processes cause this variation? Here, I analyze geographic population structure and genome-wide patterns of variation in the Rufous, Allen’s, and Calliope Hummingbirds (Selasphorus rufus/Selasphorus sasin/Selasphorus calliope) and assess evidence that linked selection on the Z chromosome drives patterns of genetic differentiation in a pair of hybridizing species. Demographic models, introgression tests, and genotype clustering analyses support a reticulate evolutionary history consistent with divergence during the late Pleistocene followed by gene flow across migrant Rufous and Allen’s Hummingbirds during the Holocene. Relative genetic differentiation (Fst) is elevated, and within-population diversity (π) is depressed on the Z chromosome in all interspecific comparisons. The ratio of Z to autosomal within-population diversity is much lower than that expected from population size effects alone, and Tajima’s D is depressed on the Z chromosome in S. rufus and S. calliope. These results suggest that conserved structural features of the genome play a prominent role in shaping genetic differentiation through the early stages of speciation in northern Selasphorus hummingbirds, and that the Z chromosome is a likely site of genes underlying behavioral and morphological variation in the group.

Select patients with metastatic clear-cell renal-cell carcinoma can be treated without systemic therapy, yet few studies have explored this population. We investigated the efficacy of metastasis-directed therapy without systemic therapy in oligometastatic clear-cell renal-cell carincoma. This investigator-initiated single-arm, phase 2 trial enrolled patients aged 18 years or older with an Eastern Cooperative Oncology Group performance status of 0–2, histologically confirmed clear-cell renal-cell carcinoma, and one to five metastases. Patients remained off systemic therapy and underwent metastasis-directed therapy to all disease sites, with additional metastasis-directed therapy for limited progression. Co-primary endpoints were progression-free survival based on Response Evaluation Criteria in Solid Tumours version 1.1 (RECIST 1.1) in the per-protocol population (patients who received radiation to at least one metastatic lesion during their initial local treatment) and systemic therapy-free survival in the intention-to-treat population. Progression-free survival was defined as the interval from enrolment to the first instance of disease progression, according to RECIST 1.1, or clinical progression, or death from any cause. Systemic therapy-free survival was defined as time from enrolment to initiation of systemic therapy or death from clear-cell renal-cell carcinoma. A prespecified 24-month median systemic therapy-free survival was the threshold for success. Safety was analysed in the per-protocol population. This trial is registered with ClinicalTrials.gov, NCT03575611, and is closed to new patient enrolment. Between July 13, 2018, and May 2, 2023, 121 patients were enrolled and included in the intention-to-treat population, of whom 120 received at least one round of definitive radiotherapy and were included in the per-protocol and safety populations. Median follow-up time for the 121 enrolled patients was 36·3 months (IQR 26·5–51·1). Median progression-free survival was 17·7 months (95% CI 14·9–22·4), and median systemic therapy-free survival time was 34·0 months (28·3–54·1). The median and lower bound of 95% CI of the median systemic therapy-free survival time exceeded the prespecified 24-month target. Eight (7%) of 120 patients had grade 3–4 adverse events at least possibly attributable to metastasis-directed therapy. The most common grade 3 event was pain near the treatment site (four events). The single grade 4 event was hyperglycaemia. There were no treatment-related deaths. Select patients with oligometastatic disease can be managed with serial metastasis-directed therapy with prolonged time off systemic therapy, favourable progression-free survival, and limited adverse events. Cancer Prevention and Research Institute of Texas, US National Cancer Institute, and Myriad Genetics.

Abstract Real geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result, many methods of analyzing genetic data assume that samples are a random draw from a well-mixed population, but are applied to clustered samples from populations that are structured clinally over space. Here, we use simulations of populations living in continuous geography to study the impacts of dispersal and sampling strategy on population genetic summary statistics, demographic inference, and genome-wide association studies (GWAS). We find that most common summary statistics have distributions that differ substantially from those seen in well-mixed populations, especially when Wright’s neighborhood size is < 100 and sampling is spatially clustered. “Stepping-stone” models reproduce some of these effects, but discretizing the landscape introduces artifacts that in some cases are exacerbated at higher resolutions. The combination of low dispersal and clustered sampling causes demographic inference from the site frequency spectrum to infer more turbulent demographic histories, but averaged results across multiple simulations revealed surprisingly little systematic bias. We also show that the combination of spatially autocorrelated environments and limited dispersal causes GWAS to identify spurious signals of genetic association with purely environmentally determined phenotypes, and that this bias is only partially corrected by regressing out principal components of ancestry. Last, we discuss the relevance of our simulation results for inference from genetic variation in real organisms.

We mapped a human deafness locus DFNB36 to chromosome 1p36.3 in two consanguineous families segregating recessively inherited deafness and vestibular areflexia. This phenotype co-segregates with either of two frameshift mutations, 1988delAGAG and 2469delGTCA, in ESPN, which encodes a calcium-insensitive actin-bundling protein called espin. A recessive mutation of ESPN is known to cause hearing loss and vestibular dysfunction in the jerker mouse. Our results establish espin as an essential protein for hearing and vestibular function in humans. The abnormal vestibular phenotype associated with ESPN mutations will be a useful clinical marker for refining the differential diagnosis of non-syndromic deafness.

In the painted bunting (Passerina ciris), a North American songbird, populations on the Atlantic coast and interior southern United States are known to be allopatric during the breeding season, but efforts to map connectivity with wintering ranges have been largely inconclusive. Using genomic and morphological data from museum specimens and banded birds, we found evidence of three genetically differentiated painted bunting populations with distinct wintering ranges and molt-migration phenologies. In addition to confirming that the Atlantic coast population remains allopatric throughout the annual cycle, we identified an unexpected migratory divide within the interior breeding range. Populations breeding in Louisiana winter on the Yucatán Peninsula and are parapatric with other interior populations that winter in mainland Mexico and Central America. Across the interior breeding range, genetic ancestry is also associated with variation in wing length, suggesting that selection may be promoting morphological divergence in populations with different migration strategies.