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Abstract BackgroundUniversal single-copy orthologs are the most conserved components of genomes. Although they are routinely used for studying evolutionary histories and assessing new assemblies, current methods do not incorporate information from available genomic data. ResultsHere, we first determine the influence of evolutionary history on universal gene content and find that across 11,098 genomes of plants, fungi, and animals comprising 2606 taxonomic groups, 215 groups significantly vary from their respective lineages in terms of BUSCO (Benchmarking Universal Single Copy Orthologs) completeness. Additionally, 169 groups display an elevated complement of duplicated orthologs, likely from ancestral whole genome duplication events. Secondly, we investigate the extent of taxonomic congruence in broad BUSCO-derived phylogenies. For 275 suitable families out of 543 tested, sites evolving at higher rates produce at most 23.84% more taxonomically concordant, and at least 46.15% less terminally variable phylogenies compared to lower-rate sites. We find that BUSCO concatenated and coalescent trees have comparable accuracy and conclude that higher rate sites from concatenated alignments produce the most congruent and least variable phylogenies. Finally, we show that undetected, yet pervasive BUSCO gene loss events lead to misrepresentations of assembly quality. To overcome this, we filter a Curated set of BUSCOs (CUSCOs) that provide up to 6.99% fewer false positives compared to the standard search and introduce novel methods for comparing assemblies using gene synteny. ConclusionsOverall, we highlight the importance of considering evolutionary histories during assembly evaluations and release the phyca software toolkit that reconstructs consistent phylogenies and offers more precise assembly assessments. 

Abstract. Urban Green Space (UGS) is vital for improving the public health and sustainability of cities. Vector data on UGS such as open data from governments and OpenStreetMap are available for retrieval by interested users, but the availability of UGS data is still limited on global and temporal scales. This study develops the UGS Extractor, a web-based application for the automatic extraction of UGS given user inputs of Area of Interest and Date of Interest. To accommodate various types of green spaces, such as parks or lawns, the application additionally allows users to set parameters for the minimum size of each UGS and the Minimum Urban Neighbor Density, enabling customization of what qualifies as UGS. The UGS Extractor implements a methodological framework that applies object-based image processing, edge detection and extraction, and image neighborhood analysis on the near real-time 10m Dynamic World collection of Land Use/Land Cover images. The application’s utility was demonstrated through two case studies. In the first, the UGS Extractor accurately mapped major parks when compared to open data sources in New Orleans, USA. In the second, the UGS Extractor demonstrated significant increases in the total area of UGS from 2015 to 2023 in Songdo, South Korea, which consequently improved green space accessibility. These results underscore the UGS Extractor’s utility in extracting specific types of UGS and analyzing their temporal trends. This user-friendly application overall offers higher spatial resolution compared to publicly available satellite-based methods while facilitating temporal studies not possible with vector datasets. 

Climate change may be a major threat to biodiversity in the next 100 years. Although there has been important work on mechanisms of decline in some species, it generally remains unclear which changes in climate actually cause extinctions, and how many species will likely be lost. Here, we identify the specific changes in climate that are associated with the widespread local extinctions that have already occurred. We then use this information to predict the extent of future biodiversity loss and to identify which processes may forestall extinction. We used data from surveys of 538 plant and animal species over time, 44% of which have already had local extinctions at one or more sites. We found that locations with local extinctions had larger and faster changes in hottest yearly temperatures than those without. Surprisingly, sites with local extinctions had significantly smaller changes in mean annual temperatures, despite the widespread use of mean annual temperatures as proxies for overall climate change. Based on their past rates of dispersal, we estimate that 57–70% of these 538 species will not disperse quickly enough to avoid extinction. However, we show that niche shifts appear to be far more important for avoiding extinction than dispersal, although most studies focus only on dispersal. Specifically, considering both dispersal and niche shifts, we project that only 16–30% of these 538 species may go extinct by 2070. Overall, our results help identify the specific climatic changes that cause extinction and the processes that may help species to survive. 

Abstract Urban evolutionary ecology is inherently interdisciplinary. Moreover, it is a field with global significance. However, bringing researchers and resources together across fields and countries is challenging. Therefore, an online collaborative research hub, where common methods and best practices are shared among scientists from diverse geographic, ethnic, and career backgrounds would make research focused on urban evolutionary ecology more inclusive. Here, we describe a freely available online research hub for toolkits that facilitate global research in urban evolutionary ecology. We provide rationales and descriptions of toolkits for: (1) decolonizing urban evolutionary ecology; (2) identifying and fostering international collaborative partnerships; (3) common methods and freely‐available datasets for trait mapping across cities; (4) common methods and freely‐available datasets for cross‐city evolutionary ecology experiments; and (5) best practices and freely available resources for public outreach and communication of research findings in urban evolutionary ecology. We outline how the toolkits can be accessed, archived, and modified over time in order to sustain long‐term global research that will advance our understanding of urban evolutionary ecology.