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An organism becomes genetically mosaic through the accumulation of somatic mutations. Genetic mosaicism is a commonality of multicellular life and has been studied extensively in humans due to its associations with aging and diseases. In humans, somatic selection shapes the accumulation of somatic mutations, with strong signatures of positive somatic selection in cancer cell lineages. So far, evidence for somatic selection in plants has been inconsistent. The evolutionary implications of genetic mosaicism in humans and other animals are limited by early specification of germline cells, preventing transmission of somatic mutations to progeny. In contrast, many plant lineages reproduce asexually with clonal progeny derived from vegetative tissues. We describe the patterns and processes shaping somatic mutation accumulation within a single, 149-year-old historic sweet orange (Citrus sinensis) tree and within a clonal lineage of sweet orange. More than 12,000 somatic mutations were identified in the historic tree and 28,000 somatic mutations were identified across 199 clonally related sweet orange accessions. Both the spatial and genomic distributions of somatic mutations are non-random. The spatial patterns of somatic mutations across the historic tree depend on tree growth and development and their accumulation across the tree canopy recapitulates branching topology. Analysis of the genomic distribution of somatic mutations revealed that the subtelomeres, which are large arrays of ~180 bp repeats, are mutation hotspots. Finally, there was genomic evidence that somatic selection shapes the accumulation of somatic mutations both within the historic tree and also during clonal propagation. 

Abstract Genomic clusters of immune genes, including those encoding nucleotide-binding leucine-rich repeat (NLR) proteins, are a model for exploring the dynamics of genomic regions in flux. Rapid sequence evolution of immune genes, including NLRs, and variation in their gene content, may enable long-lived plants, which lack adaptive immune systems, to keep pace with the fast evolution of pathogens. To explore the patterns and processes shaping the evolution of NLR gene content in a genus of long-lived tree species, we unified the annotation of NLR genes across 11 accessions (or 15 haplotypes) from the genusCitrusand its relatives, including three new diploid genome assemblies. A majority of NLRs were arranged in genomic clusters composed of paralogous genes, typically from a single gene family. Even larger clusters, with 10 or more NLRs, were limited to genes derived from one or few gene families. These patterns suggested that genomic clustering of NLRs arose through local expansion of phylogenetically related NLRs, but the mechanistic processes driving these patterns are not clear. Local gene duplication can be mediated by multiple processes, including transposon-mediated gene capture and subsequent proliferation, and non-allelic repair of double stranded breaks, including unequal recombination. Examples of retrotransposon-mediated duplication of NLRs were identified, but these were not sufficient to explain massive regional expansions. Signatures of unequal recombination are challenging to identify. Focusing on recent lineage-specific sequence duplications, at least one case of unequal recombination was identified, supporting a role for unequal recombination in shaping genomic variation in these regions. 

Southeastern California is known for complex fault networks that accommodate strain from Pacific-North American plate convergence. The 250-km-long, left-lateral Garlock fault is integral to this system, yet its overall kinematic role within the plate boundary and relationship with faults of the Eastern California shear zone/Walker Lane belt remain poorly understood. A key area that has not been adequately studied is a 15-km stretch of the eastern Garlock fault, at its intersections with the right-lateral Brown Mountain fault and left-lateral Owl Lake fault. This segment of the fault lies within the China Lake Naval Air Weapons Station and U.S. Fort Irwin boundaries, which have restrictions on civilian access and portions of which contain unexploded ordnance, making them unsuitable and unsafe for field investigations. The purpose of this project is to use a combination of high-resolution LiDAR topographic data, remotely sensed imagery, and published geochronology data to map and establish the ages of faulted landforms along this portion of the eastern Garlock fault. The inaccessibility of this area makes it ideal for the application of remote-sensing techniques. A range of surface analysis techniques were used to differentiate and map Quaternary units in the study area. Geomorphic surface properties were determined from physiographic roughness and surface reflectance data, established from analysis of LiDAR, radar backscatter, and visual-near and short-wave infrared multispectral and hyperspectral reflectance datasets. The ages of faulted landforms were established using two approaches: (1) fault scarp and terrace riser degradation analysis and (2) a surface property-age model that links remotely sensed surface properties to new and published ages of alluvial surfaces in the region. A final goal of the study was to determine the slip rate along this segment of the Garlock fault and other faults in the map area. To accomplish this, offset landforms, such as terrace risers and channels, were analyzed in the context of the new age determinations. The results will be compared to published slip rate estimates for the region in order to better understand the Garlock fault's role within the plate boundary and how plate boundary strain is being accommodated in such an intraplate setting. 

Abstract In 2023, the first Polar Postdoc Leadership Workshop convened to discuss present and future polar science issues and to develop leadership skills. The workshop discussions fostered a collective commitment to inclusive leadership within the polar science community among all participants. Here, we outline challenges encountered by underrepresented groups in polar sciences, while also noting that progress has been made to improve inclusivity in the field. Further, we highlight the inclusive leadership principles identified by workshop participants to bring to the polar community as we transition into leadership roles. Finally, insights and practical knowledge we gained from the workshop are shared, aiming to inform the community of our commitment to inclusive leadership and encourage the polar community to join us in pursuing action toward our shared vision for a more welcoming polar science future. 

Abstract Aluminum‐dependent stoppage of root growth requires the DNA damage response (DDR) pathway including the p53‐like transcription factor SUPPRESSOR OF GAMMA RADIATION 1 (SOG1), which promotes terminal differentiation of the root tip in response to Al dependent cell death. Transcriptomic analyses identified Al‐induced SOG1‐regulated targets as candidate mediators of this growth arrest. Analysis of these factors either as loss‐of‐function mutants or by overexpression in theals3‐1background shows ERF115, which is a key transcription factor that in other scenarios is rate‐limiting for damaged stem cell replenishment, instead participates in transition from an actively growing root to one that has terminally differentiated in response to Al toxicity. This is supported by a loss‐of‐functionerf115mutant raising the threshold of Al required to promote terminal differentiation of Al hypersensitiveals3‐1. Consistent with its key role in stoppage of root growth, a putativeERF115barley ortholog is also upregulated following Al exposure, suggesting a conserved role for this ATR‐dependent pathway in Al response. In contrast to other DNA damage agents, these results show that ERF115 and likely related family members are important determinants of terminal differentiation of the root tip following Al exposure and central outputs of the SOG1‐mediated pathway in Al response. 

The primary theory of software engineering is that an organiza- tion’s Policies and Processes influence the quality of its Products. We call this the PPP Theory. Although empirical software engineer- ing research has grown common, it is unclear whether researchers are trying to evaluate the PPP Theory. To assess this, we analyzed half (33) of the empirical works published over the last two years in three prominent software engineering conferences. In this sample, 70% focus on policies/processes or products, not both. Only 33% provided measurements relating policy/process and products. We make four recommendations: (1) Use PPP Theory in study design; (2) Study feedback relationships; (3) Diversify the studied feed- forward relationships; and (4) Disentangle policy and process. Let us remember that research results are in the context of, and with respect to, the relationship between software products, processes, and policies.