Molecular Biology and Evolution

MitoNGS: an online platform to analyze fish metabarcoding data in high resolution Abstract. Environmental DNA (eDNA) metabarcoding has become a powerful tool for assessing fish biodiversity in aquatic ecosystems. However, accurate specie

Zhu, @susumu31.bsky.social et al. present MitoNGS, a platform designed for high-resolution analysis of fish metabarcoding data that allows for fish detection, biodiversity monitoring, conservation research, and bioresource management.

🔗 doi.org/10.1093/molbev/msag046

#evobio #molbio

Read more on this exciting new perspective on gene function, as James McInerney explains to us how it can impact our views on evolutionary theory:

🔗 tinyurl.com/genomicperplexity

@jomcinerney.bsky.social proposes that genomes do not encode fixed functions but rather “probability distributions” over functional and phenotypic outcomes, and introduces “genomic perplexity” as a measure of gene-context incompatibility.

🔗 doi.org/10.1093/molbev/msag041

#evobio #molbio

MBE | Mammalian mitochondrial DNA accumulates insertions and deletions with age in energetically demanding tissues

@edmundotogo.bsky.social et al. studied de novo indel mtDNA mutations across multiple age groups in three mammalian species, showing that indels accumulate rapidly with age in somatic tissues with high energetic demand or high proliferation.

🔗 doi.org/10.1093/molb...

#evobio #molbio #mtDNA

Congratulations Catherine!

Regulatory features determine the evolutionary fate of laterally acquired genes in plants Abstract. Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. How

Ecstatic to see the first chapter of my PhD published in MBE!
Most laterally acquired genes in plants are degenerating - the retained genes may to be more successful because they bring over their own regulatory machinery
academic.oup.com/mbe/article/...

April Fools’ Day is coming early this year, but really, any day is a good day to poke fun at the system.
Well done @russcd.bsky.social

I’m already getting community feedback on the core-pivotal index. I truly appreciate it. But in the spirit of core-pivoteering, I will only implement suggestions from whoever has the highest core-pivotal index.

"All granting agencies should immediately switch to [...] the core-pivotal index where all available funds are assigned to the individual with the highest value and all others receive none. Furthermore, hiring committees should ignore research subject, teaching, fit, and all other contributions."

"The defining goal of the academic endeavor is to establish a single perfect value that completely summarizes entire careers’ achievements. Such an index would allow the academic community to formally and uncontroversially determine the best researchers by simply comparing their respective scores."

The core-pivotal index: a geometry-first approach to academic impact The defining goal of the academic endeavor is to establish a single perfect value that completely summarizes entire careers’ achievements. Such an index wo

@russcd.bsky.social ushers in a new era of academic metrics with the core-pivotal author index, which assigns all credit to authors that occupy the exact center of the author list, while non-central peripheral authors receive no credit whatsoever.

🔗 doi.org/10.1093/molbev/msag026

#evobio #molbio

“It takes a vigilant community to guard against the growth of malfeasance in the academic publishing environment, and society-owned journals like MBE must take a leading role. Along with the core responsibility of dissemination and as a repository of the scientific record, we must be vigilant in safeguarding the reliability of the scientific record to ensure the long-term durability of science as a method of knowing.” Claudia Russo and Brandon Gaut MBE Editors-in-Chief

“We are extremely proud of the manuscripts published in MBE. MBE is a highly respected journal within and beyond our immediate molecular evolutionary community. It remains so because of our vibrant and active volunteer community of reviewers and editors, whom we applaud for their willingness to support a society-owned, non-profit journal in an environment of ever-escalating for-profit journals.” Claudia Russo and Brandon Gaut MBE Editors-in-Chief

MBE | The role of society journals in protecting the scientific record

MBE Editors-in-Chief Claudia Russo and Brandon Gaut publish a new editorial on the role of society journals in protecting the scientific record.

🔗 doi.org/10.1093/molbev/msag022

#evobio #molbio #societyjournal

@claurusso.bsky.social @bsgaut.bsky.social

Thank you, James, for another great contribution to our journal!

Visit our website to learn why publishing with MBE, as a society-owned journal, helps to support evolutionary science:
🔗 academic.oup.com/mbe/pages/why-publish

Molecular Biology and Evolution A new look, the same rigor and commitment to the community

🙌 The new logo of Molecular Biology and Evolution is now live!

This new look will carry us forward while maintaining the same rigor and commitment to the molecular evolutionist community as an SMBE journal.

#evobio #molbio #science #biology #societyjournal

Leveraging low-cost short-read sequencing: revolutionizing complex trait genetics Abstract. The genetics of complex traits has been fundamentally transformed by the dramatic reduction in short-read sequencing costs, leading to a dramatic

Ruckman & Long review how affordable sequencing is transforming complex trait research, focusing on how affordable sequencing has fundamentally reshaped what questions evolutionary researchers can ask and how they can answer them.

🔗 doi.org/10.1093/molbev/msag025

#evobio #molbio

Authors on Bluesky
@corncolors.bsky.social
@kdyerlab.bsky.social
@arburga.bsky.social
@cecilecourret.bsky.social
@anabferretti.bsky.social
@emilianomarti.bsky.social
@laurarossevo.bsky.social
@fungage-lab.bsky.social

MBE | The evolutionary genomics of meiotic drive Meiotic drivers gain transmission advantages by distorting equal, Mendelian segregation. This review discusses the evolutionary genomics of meiotic drive. The figure highlights the interactions of meiotic drive elements with other classes of selfish genetic elements including: direct interactions between drivers and transposable elements (TEs) (A) or satellites (C) that can facilitate the spread of drivers; other drive systems that cause the mutual destruction of all gametes (B; e.g. the presence of multiple toxin-antidote systems); indirect interactions where the host machinery responsible for silencing TEs are recruited to silence drivers (D); dosage-sensitive interactions involving sex-linked drivers that result in gene amplifications (E); and tradeoffs between suppressing drive and TEs (F).

For a new MBE Review, Presgraves et al. argue that many features of genome evolution, content, and organization seemingly inexplicable by adaptation or nearly neutral processes are instead best accounted for by meiotic drive.

🔗 academic.oup.com/mbe/article/...

#evobio #molbio

Authors on Bluesky
@paulineraim.bsky.social
@emilyrbaker.bsky.social
@luketdunning.bsky.social

Regulatory features determine the evolutionary fate of laterally acquired genes in plants Abstract. Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. How

Collins et al. combined expression, methylation, and genomic data to investigate long-term persistence of laterally acquired genes in the grass Alloteropsis, showing that those capable of regulating their own expression are more likely to persist.

🔗 doi.org/10.1093/molbev/msag042

#evobio #molbio

Genomic Perplexity and the Evolution of Context-Dependent Function Abstract. The fundamental principle that selection acts on a gene’s function often assumes implicitly that this function is fixed and intrinsic. However, e

New paper out in MBE! 🧵
"Genomic Perplexity and the Evolution of Context-Dependent Function"
The big idea: genes don't have fixed functions. Function emerges from context - genomic, cellular, environmental. And we can quantify this. academic.oup.com/mbe/article/...

Authors on Bluesky
@vascularinfection.bsky.social
@pcicuta.bsky.social
@bspenman.bsky.social

Invasion preferences suggest a possible role for Plasmodium falciparum parasites in the expansion of Duffy negativity in West and Central Africa Abstract. Duffy antigen receptor for chemokines (DARC) is the primary red blood cell (RBC) receptor for invasion of human RBCs by Plasmodium vivax and Plas

Manneh et al. used flow cytometry and microscopy-based approaches to investigate whether P. falciparum parasites preferentially invade specific Duffy RBC phenotypes and explored two potential explanations for invasion preference

🔗 doi.org/10.1093/molb...

#evobio #molbio #malaria

MBE | Phylogenetic Analysis of NEAT1 and MALAT1 Long Non-Coding RNAs Highlights Structure–Function Relationships in Paraspeckle Biology

Arkhipova & Drukker identified orthologs of NEAT1 and MALAT1 - the only lncRNAs that use the tRNA-processing machinery for maturation - across 545 mammals to investigate differences in function and evolutionary conservation.

🔗 doi.org/10.1093/molbev/msaf265

#evobio #molbio

The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability Abstract. Spontaneous mutations are the primary source of genetic variation and play a central role in shaping evolutionary processes. To investigate mutat

Deng et al. assembled the first chromosome-level reference genome for Daphnia obtusa and deep sequenced eight mutation-accumulation lines for ~500 generations, assessing the interplay among mutation, selection, and genome stability.

🔗 doi.org/10.1093/molb...

#evobio #molbio

MBE | Amhy/Amhr2y-mediated sex determination in two distantly related teleosts relies on the conserved Alk3-Smad5 axis

Zhou et al. establish Alk3 and Smad5 as essential and specific transducers of the Amhy/Amhr2-mediated sex-determination pathway, revealing a potentially conserved signaling axis across teleosts.

🔗 doi.org/10.1093/molbev/msag038

#evobio #molbio

MBE | Evolutionary remodeling of the FXR binding pocket drove functional divergence and ligand discrimination

Yamamoto, @cdokafor.bsky.social et al. used structural and functional analysis to identify the set of evolutionary substitutions that recapitulate the shift in ligand preference from the FXR/LXR ancestor to the ancestral vertebrate FXR.

🔗 doi.org/10.1093/molbev/msag031

#evobio #molbio

Genetic formation and regional disparities of Kra–Dai and Hmong–Mien speakers inferred from ancient genomes of cave burial populations in southwest China Abstract. Cave burial is a funerary practice believed to be associated with modern Kra–Dai (KD) and Hmong–Mien (HM) speakers for thousands of years. Howeve

Tao et al. sequenced 14 ancient genomes from cave burial sites in Guangxi, revealing continuous gene flow from northern lineages into ancient cave burial populations.

🔗 doi.org/10.1093/molbev/msag034

#evobio #molbio #humanevolution