Biology subjects

McDaniel, S.

Publications and source records attributed to McDaniel, S..

5 recordsLinked to original sources

bioRxiv2026

Gene model for the ortholog of raptor in Drosophila eugracilis

Gene model for the ortholog of raptor in the D. eugracilis Apr. 2013 (BCM-HGSC/Deug_2.0) (DeugGB2) Genome Assembly (GenBank Accession: GCA_000236325.2) of Drosophila eugracilis. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

bioRxiv2026

UVfinder: a tool to extract bryophyte sex-linked gene copies from the GoFlag408 probe set

PremiseTarget enrichment sequencing using probe sets like GoFlag 408 has revolutionized phylogenetics, yet recent genomic data indicate that some probes may be sex-linked, potentially introducing topological conflict but also allowing studies of sex-specific evolutionary processes. To test for sex-linkage across the bryophytes, we developed UVfinder, a pipeline designed to identify sex-linked GoFlag loci across published moss genomes and enable sex-aware downstream analyses. Methods and ResultsApplying UVfinder to 50 dioicous moss genomes,we identified 93 probes that exhibit sex-linkage in one or more lineages. Our results provide genomic evidence for neo-sex chromosome formation via autosome-sex chromosome fusion and gene translocation. By comparing species trees derived from sex-linked versus autosomal loci in Hypnales and Dicranidae, we demonstrate that sex-linked loci harbor phylogenetic information that is distinct from that in autosomes. We also discovered a pervasive female sampling bias perhaps reflecting a preference among collectors for plants with sporophytes. ConclusionsOur findings highlight the dynamism in sex linkage across bryophytes and suggest that sex-aware phylogenomics can be used to reconstruct ancestral karyotypes and potentially resolve topological conflict. We also expect that UVfinder will facilitate study of sex specific evolutionary processes, particularly with improved genome assemblies and increased sampling in males.

bioinformatics↗

bioRxiv2021

MBNL1 and RBFOX1 co-regulate alternative splicing events transcriptome-wide through a conserved buffering mechanism

Alternative splicing (AS) is controlled by cis-regulatory elements recognized by networks of trans-acting factors. Here we investigate modes and mechanisms of AS co-regulation by MBNL1 and RBFOX1, two RNA binding proteins (RBPs) critical for developmental AS transitions. We generated two cell models that express each RBP under separate inducible promoters. Transcriptome-wide categorization of the impacts of RBFOX1 expression on MBNL1 splicing revealed a common co-regulatory mode through which RBFOX1 buffers MBNL1 dose-dependent splicing regulation by reducing the total range of exon inclusion or exclusion. Minigene mutational analysis and in vitro binding experiments suggest that this buffering mechanism occurs through a shared cis-regulatory element previously unidentified as critical for MBNL1-dependent activity. Overall, our studies define a conserved co-regulatory mechanism through which RBFOX1 and MBNL1 can fine-tune and provide redundancy for AS outcomes. These studies indicate overlapping use of RNA motifs with potential implications for when activity of RBPs is disrupted.

biochemistry↗

bioRxiv2020

Chromosome fusions shape an ancient UV sex chromosome system

Non-recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration1,2. The correlation between suppressed recombination and degeneration is clear in animal XY systems1,2, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions3,4. Here we test for degeneration in the bryophyte UV sex chromosome system through genomic comparisons with new female and male chromosome-scale reference genomes of the moss Ceratodon purpureus. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes show signs of weaker purifying selection than autosomes, we find suppressed recombination alone is insufficient to drive gene loss on sex-specific chromosomes. Instead, the U and V sex chromosomes harbor thousands of broadly-expressed genes, including numerous key regulators of sexual development across land plants.

evolutionary biology↗

bioRxiv2016

Silversword and lobeliad reintroduction linked to landscape restoration on Mauna Loa and Kilauea, and its implications for plant adaptive radiation in Hawaii

The endemic Hawaiian silversword and lobeliad lineages, which are two of the worlds premier examples of plant adaptive radiation, exemplify the severity of the threats confronting the Hawaiian flora, especially the threats posed by alien species. We have implemented collaborative reintroduction efforts with the endangered Ka[u] silversword (Argyroxiphium kauense) and Pele lobeliad (Clermontiapeleana) in Hawaii Volcanoes National Park. The efforts with the Ka[u] silversword have involved rediscovery, helicopter assisted rescue of diminutive remnant founders, managed breeding, outplanting at two sites in the Park of more than 21,000 seedlings deriving from 169 founders, and facilitated achene dispersal following flowering. The efforts with the Pele lobeliad have involved rediscovery, air-layering of remnant founders while suspended on climbing ropes, managed breeding, and outplanting at two sites in the Park of more than 1,000 seedlings (to date) deriving from six of the seven known founders. We have linked the reintroduction efforts to landscape restoration at large scales in the Park and in adjacent State and private lands, thereby increasing the opportunities for substantial population growth and expansion of the Ka[u] silversword and Pele lobeliad in the future. Additionally, we have extended the reintroduction efforts, including the link to landscape restoration, to encompass all other endangered silversword and lobeliad taxa occurring historically on the eastern slopes of Mauna Loa or on K[i]lauea. In so doing, we seek to restore the possibility of adaptive radiation of the silversword and lobeliad lineages going forward, especially on the youngest and most geologically active, and thus perhaps most evolutionarily dynamic, part of the Hawaiian archipelago.\n\nDedicationThis paper celebrates the centennial of Hawaii Volcanoes National Park, which was founded in August 1916.

evolutionary biology↗