Biology subjects

Gazda, M. A.

Publications and source records attributed to Gazda, M. A..

7 recordsLinked to original sources

bioRxiv2026

Preprint solicitation as a natural experiment in scholarly publishing

Preprinting is a growing and increasingly recognized mechanism for scientific communication and productivity and a way to facilitate global access to science. The interplay of preprinting practices with formal peer-reviewed publication is an open question that is now tractable to targeted analysis. Here, we take advantage of nearly a decade of preprint solicitation at Proceedings B to address this question, which offers a quasi-experimental setting for comparing outcomes for solicited preprints and traditionally submitted manuscripts. We used submission records from 15,368 manuscripts from 2018-2024 to assess whether preprint solicitation affects acceptance rates, journal scope, author geographic diversity, and post-publication uptake. Solicited manuscripts were accepted at nearly twice the rate of traditional submissions and received more downloads and citations after publication. Submission topics were broadly similar between the two routes, though solicited manuscripts showed marginally greater subject diversity. Geographic disparities favoring the Global North persisted, but acceptance rates for solicited manuscripts converged across regions, narrowing the gap seen in traditional submissions. These findings extend earlier work on this initiative and indicate that editor-driven solicitation can identify high-quality preprints, broaden geographic representation, and increase research visibility, offering a replicable model for journals seeking to diversify authorship while maintaining editorial standards.

scientific communication and education↗

bioRxiv2026

ARTIFICIAL SELECTION DIVERSIFIES BIRDSONG THROUGH POLYGENIC CHANGES ACROSS SENSORY AND MOTOR SYSTEMS

Vocal learning, or the ability to acquire and produce contextualized sounds through social interaction, underlies human speech yet has evolved in a few animal lineages, including songbirds. In songbirds, learned song is produced by a dedicated neural circuit and depends on auditory feedback for its acquisition and maintenance. Roughly four centuries of artificial selection on the domestic canary (Serinus canaria) have produced song breeds whose vocalizations diverge as much as those of distinct species, offering a rare intraspecific system in which to identify the genetic and neural changes underlying vocal divergence. Here we show that selection for song reshaped the canary song control system. Compared with breeds selected for plumage or body form, song breeds show increased neural progenitor proliferation and breed-specific changes in neuronal recruitment, sensorimotor brain region volume, and auditory sensitivity. Genome-wide analyses reveal a polygenic architecture underlying song divergence, enriched for transcriptional regulation and synaptic transmission genes. Among these, we find a coding variant in ADGRV1, the gene mutated in human Usher syndrome type 2C, associated with low-frequency singing and elevated auditory thresholds in canary. Disrupting ADGRV1 in zebrafish alters hair cell dynamics, linking adgrv1 mutation to a peripheral sensory mechanism. These findings demonstrate that learned vocal behavior can diversify rapidly through changes spanning sensory, neurogenic, and motor systems, with hearing itself as a substrate for selection.

evolutionary biology↗

bioRxiv2024

Reporting quality of quantitative polymerase chain reaction (qPCR) methods in scientific publications

Reproducibility is a significant concern in scientific research and complex methods like quantitative polymerase chain reaction (qPCR) demand stringent reporting standards to ensure that the methods are reproducible, data are sound, and conclusions are trustworthy. Although the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines were introduced in 2009 to improve qPCR reporting, a 2013 study identified ongoing deficiencies that hinder reproducibility. To further investigate the transparency and completeness of qPCR reporting, we systematically assessed articles published in the top 20 journals in genetics and heredity (n=186) and plant sciences (n=246) that used qPCR. Our analysis revealed frequent omissions and inadequate specification of critical information necessary for evaluating and replicating qPCR experiments. RNA integrity, along with assessment methods and instruments used to assess it, are seldom reported. Although primer sequences are often disclosed, names and accession numbers of housekeeping genes are frequently omitted. Additionally, essential details about RNA extraction, RNA-to-cDNA conversion, and qPCR, such as kit names, catalog numbers, and reagent information, are often missing. Our findings underscore the urgent need for improved reporting practices in qPCR experiments, emphasizing quality controls, detailed descriptions of reagents and materials, and greater analytical transparency. Addressing these reporting deficiencies is crucial for enhancing the reproducibility and evaluating the trustworthiness of qPCR research. Potential solutions include encouraging authors to cite protocols published in online repositories, providing reporting templates, or developing automated tools to check reporting compliance.

genetics↗

bioRxiv2024

Convergent gene expression in epithelial cells illuminates the evolution of uterine receptivity

The epithelium of the uterine endometrium is the first maternal interface encountered by the embryo, and plays crucial roles in the maternal-embryonic crosstalk necessary to embryo implantation. Mechanisms of embryo implantation are highly variable between mammals: humans and mice have convergently evolved similar embryo implantation phenotypes, where the embryo embeds in the maternal mucosa, which differs from the ancestral mammalian and primate phenotypes. This phenomenon is thought to be partly controlled by maternal epithelial receptivity signals during the window of implantation. Here, we combined endometrial epithelial organoid models and single-cell transcriptomics to investigate how gene expression has evolved in endometrial epithelial cells between human, non-human primates and mouse at key time points in the hormonal cycle. We discovered that many maternal genes involved in uterine receptivity and embryo implantation exhibit more similar expression patterns between human and mouse compared to macaque and marmoset. In particular, we show that the endometrial expression of LIF, a crucial actor of endometrial receptivity in both human and mouse, is likely an evolutionary convergence rather than a conserved feature as previously hypothesised.

evolutionary biology↗

bioRxiv2021

Evidence of post-domestication hybridization and adaptive introgression in Western European grapevine varieties

Grapevine (Vitis vinifera L.) is one of the most significant crops in the world. Todays richness in grapevine diversity results from a complex domestication history over multiple historical periods. Here, we employed whole genome resequencing to elucidate different aspects of the recent evolutionary history of this crop. Our results support a model in which a central domestication event in grapevine was followed by post-domestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties, which show large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by geneflow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.

plant biology↗

bioRxiv2020

Creating Clear and Informative Image-based Figures for Scientific Publications

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in three fields; plant sciences, cell biology and physiology (n=580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.

bioinformatics↗

bioRxiv2019

Genetic Basis Of De Novo Appearance Of Carotenoid Ornamentation In Bare-Parts Of Canaries

AO_SCPCAPBSTRACTC_SCPCAPUnlike wild and domestic canaries (Serinus canaria), or any of the three dozen species of finches in genus Serinus, the domestic urucum breed of canaries exhibits bright red bills and legs. This novel bare-part coloration offers a unique opportunity to understand how leg and bill coloration evolve in birds. To identify the causative locus, we resequenced the genome of urucum canaries and performed a range of analyses to search for genotype-to-phenotype associations across the genome. We identified a nonsynonymous mutation in the gene BCO2 (beta-carotene oxygenase 2, also known as BCDO2), an enzyme involved in the cleavage and breakdown of full-length carotenoids into short apocarotenoids. Protein structural models and in vitro functional assays indicate that the urucum mutation abrogates the carotenoid cleavage activity of BCO2. Consistent with the predicted loss of carotenoid cleavage activity, urucum canaries had increased levels of full-length carotenoid pigments in bill tissue and a significant reduction in levels of carotenoid cleavage products (apocarotenoids) in retinal tissue compared to other breeds of canaries. We hypothesize that carotenoid-based bare-part coloration might be readily gained, modified, or lost through simple switches in the enzymatic activity or regulation of BCO2 and this gene may be an important mediator in the evolution of bare-part coloration among bird species.

evolutionary biology↗