David Alvarez‐Ponce

A high-quality draft genome assembly of Johnsongrass illuminates relationships between polyploidization, crop-wild hybridization, and reproductive biology

Melinda K. Yerka, Julia N Trowbridge, David Alvarez‐Ponce, Deepti Nigam et autres

Johnsongrass [Sorghum halepense (L.) Pers.] is an allopolyploid, rhizomatous, perennial grass species and one of the most troublesome weeds in global agriculture. We assembled the first Johnsongrass genome to clarify poorly understood genetic factors influencing variable rates of crop-wild hybridization with cultivated …

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The publication and citation gender gap in biology: bibliometric analysis of biology faculty at top United States universities

David Alvarez‐Ponce, James Vesper

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Supplementary_Tables_Huchon_at_al_2026

Dorothee Huchon, Soojin V. Yi, David Alvarez‐Ponce, Ismam Ahmed Protic et autres

Supplementary tables from:No Support for DNA Cytosine Methylation in Myxosporean GenomesDorothée Huchon, Dongmin R. Son, Ismam Ahmed Protic, Tatiana Orli Milkewitz Sandberg, Soojin V. Yi, David Alvarez-Ponce. Supplementary tables provided:Table S2: Phylogenetic trees generated.Table S7: Accession numbers and E-values of the best …

Supplementary_Tables_Huchon_at_al_2026

Dorothee Huchon, Soojin V. Yi, David Alvarez‐Ponce, Ismam Ahmed Protic et autres

Supplementary tables from:No Support for DNA Cytosine Methylation in Myxosporean GenomesDorothée Huchon, Dongmin R. Son, Ismam Ahmed Protic, Tatiana Orli Milkewitz Sandberg, Soojin V. Yi, David Alvarez-Ponce. Supplementary tables provided:Table S2: Phylogenetic trees generated.Table S7: Accession numbers and E-values of the best …

Comparative genomic analyses shed light on the introduction routes of rice-pathogenic Burkholderia gladioli strains into Bangladesh

Ismam Ahmed Protic, Mohammed Nasir Uddin, Andrew J. Gorzalski, Md. Rashidul Islam et autres

ABSTRACT Background The gram-negative bacterium Burkholderia gladioli can cause diseases in a wide range of hosts, including humans and plants. In rice, it produces Bacterial Panicle Blight (BPB), an emerging disease that is threatening the production of this staple food worldwide. Recently, …

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Introgressed Variants Obscure Phylogenetic Relationships but Are Not Subject to Positive Selection in Australasian Long-Tailed Parrots

Brian Tilston Smith, Agusto Luzuriaga-Neira, David Alvarez‐Ponce, Kaiya L. Provost et autres

Gene flow often obscures phylogenetic relationships, but the evolutionary significance of introgressed variants is unclear. Here, we examine the Australasian long-tailed parrots (Psittaculinae: Polytelini) in which an unexpected sister relationship between Polytelis alexandrae and the genus Aprosmictus, and not the other Polytelis …

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Roles and Future Opportunities for Genomic Architecture in Understanding Repeated Evolution

Riley Kellermeyer, David Alvarez‐Ponce, Javier Arsuaga, Frédéric J. J. Chain et autres

The trajectory of evolution is impacted by molecular constraints and biases that are difficult to validate experimentally. Repeated evolution of similar traits across the Tree of Life serves as a natural experiment to discern common factors that drive the evolution of these …

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Do Manuscripts by Female Evolutionary Biologists Spend Longer Under Review?

David Alvarez‐Ponce, James Vesper

Women are under-represented in academia and in STEM careers, especially at senior positions and top institutions. This may be, at least in part, due to the many obstacles that they experience along the academic pipeline. There has been substantial debate as to …

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Organismal complexity strongly correlates with the number of protein families and domains

David Alvarez‐Ponce, Krishnamurthy Subramanian

In the pregenomic era, scientists were puzzled by the observation that haploid genome size (the C-value) did not correlate well with organismal complexity. This phenomenon, called the "C-value paradox," is mostly explained by the fact that protein-coding genes occupy only a small …

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Asymmetrical Evolution of Promoter Methylation of Mammalian Genes after Duplication

Mercedes de la Fuente, Isabel Mendizabal, Mira Han, Soojin V. Yi et autres

Even though gene duplication is a key source of new genes and evolutionary innovation, it is unclear how duplicates survive the period immediately following gene duplication, in which both copies are functionally redundant. In the absence of epigenetic silencing, the abundance of …

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First complete genome sequence of a Bacterial Panicle Blight causing pathogen, Burkholderia glumae, isolated from symptomatic rice grains from Bangladesh

Ismam Ahmed Protic, Md. Nasir Uddin, Abu Sina Md. Tushar, Shah Tasdika Auyon et autres

OBJECTIVES: Rice (Oryza sativa) is the most important food for more than two thirds of the world's population. Bangladesh is the third largest producer and consumer of rice globally. Recently, several symptoms of Bacterial Panicle Blight (BPB) in rice, including seedling blight, …

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Highly Abundant Proteins Are Highly Thermostable

Agusto Luzuriaga-Neira, Andrew M. Ritchie, Bryan L Payne, Oliver Carrillo et autres

Highly abundant proteins tend to evolve slowly (a trend called E-R anticorrelation), and a number of hypotheses have been proposed to explain this phenomenon. The misfolding avoidance hypothesis attributes the E-R anticorrelation to the abundance-dependent toxic effects of protein misfolding. To avoid …

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