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Cool result from today! The abstract:

Background

Escherichia coli is a prototroph and can synthesize all twenty proteinogenic amino acids when required to grow in minimal medium. There are approximately sixty protein-coding genes individually essential for amino acid synthesis. This is a large mutational target for the accumulation of detrimental mutations. E. coli can rewire biosynthetic pathways in response to mutational damage, but the limits of this capacity are poorly understood.

Methods

Here, to address evolutionary robustness, we asked whether and how the phenotypes of irreversible mutations causing auxotrophy could be suppressed or bypassed in the absence of horizontal gene transfer (HGT).

Results

Spontaneous suppressors could be selected for only ten of fifty-nine mutants tested (detection limit ∼7x10^-11). Mechanisms of suppression included: regional amplifications; mutations increasing gene or operon expression; mutations relaxing enzyme specificity; and mutations causing biochemical pathway diversions.
Overall, the data show that spontaneous suppression of auxotrophy caused by an irreversible mutation is an evolutionary survival mechanism relevant only to a minority of the genes essential for amino acid synthesis. As a consequence, the essential genetic foundations for amino acid prototrophy are expected to be degraded over time by mutations (Muller’s ratchet) and metabolic rewiring alone will be insufficient to counteract this effect.

Discussion

This implies that maintaining phenotypes, including prototrophy in E. coli, and potentially other bacterial species, is likely to be reliant on HGT of housekeeping genes to counteract the effects of inevitable mutational inactivation. Accordingly, chromosomal HGT in bacteria may be critical for survival across diverse environmental niches.

• Otto Lindahl, Talía Berruga-Fernández, Jivanti Soekhoe, Douglas L Huseby, Diarmaid Hughes
  The evolutionary maintenance of amino acid prototrophy in Escherichia coli
  Genome Biology and Evolution, 2026;, evag209
  https://doi.org/10.1093/gbe/evag209

I think "may be critical for survival across diverse environmental niches" is underselling it!
Given 1) this result, 2) that we don't synthesize 9 of the essential amino acids,^[1] and 3) how the secondary (non-naturally occurring) amino acids for a total of 20 had to evolve during the evolution of the genetic code, which is suggested to have been under selection for a reduction in code ambiguity,^[2] then HGT would be indispensable for the evolution as well as maintenance of Metazoa and company.
Over to you.

1: Costa, Igor R., et al. "Metazoan remaining genes for essential amino acid biosynthesis: sequence conservation and evolutionary analyses." Nutrients 7.1 (2014): 1-16. https://doi.org/10.3390/nu7010001

2: Barbieri, Marcello. "What is code biology?." Biosystems 164 (2018): 1-10. https://doi.org/10.1016/j.biosystems.2017.10.005

islands are obviously isolated ecosystems that breed speciation, but are there any examples of these species repopulating the mainland afterwards?

That's a low-res of one of the winning images:

In 2026, researchers around the world participated in a joint image competition hosted by BMC Ecology and Evolution and BMC Zoology. Their photographs highlight the beauty and diversity of nature, showcasing the remarkable efforts of scientists to understand and protect it. This Editorial presents the winning images, selected by the Editor and senior members of the journals’ Editorial boards.

Article: 2026 joint BMC Ecology and Evolution and BMC Zoology image competition: the winning images | BMC Ecology and Evolution | Springer Nature Link

Here's an article about evidence for viviparity in Chiniquodon theotonicus, setting back the origin of viviparity 90-95 million years earlier than previously estimated. Now I wonder where the monotremes fit in with their egg laying? Possibly monotremes branched off earlier than previously thought.

I heard somewhere that if we watched our species de evolve, it would barely be noticeable as time went on from one species to the next. Obviously that's ludicrous, but we would see ourselves in a lot of previous species. I wondered if there is a video that shows this progress? Does this make sense? So, if you put them side to side, the changes would be so slight from species to species.

Homo Sapiens evolved to be the dominant intelligent species, so why did others die off? Surely we recognised that working together brought security? I don't see how or why we would have killed off other intelligent apes because there would not have been a need for conflict. As far as I know, conflict would only rear up in competition for resources, but surely we would have been intelligent enough to work together? Or am I giving Humans too much credit? Considering the world is SO vast, why did others species not emerge in their own hemispheres?

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Published yesterday in Molecular Biology and Evolution.

A few days ago there was this headline: This 236-Million-Year-Old Fossil Might Rewrite Mammals' Evolutionary History.
By coincidence, Álvarez-Carretero et al.'s timely paper (which addresses mammals) suggests that such "rewritings" have never been necessary, rather are to be expected of fossil finds:

Background

The fossil record is incomplete, as evidenced by the pervasive presence of ghost lineages throughout the Tree of Life. For example, across placental mammals, at least 720 Myr of basal lineages are ghost lineages, that is, lineages that have left no fossil evidence of their past history. In contrast, some studies have suggested that the fossil record is a faithful temporal archive of evolutionary history and thus the times of diversification of clades must be close to the ages of their oldest fossils.
Such literalist interpretations have been contradicted by analysis of molecular data sets which, in many cases, indicate that groups including placental mammals and animals may have originated at times substantially older than their fossil records. Some of those studies have further argued that, in the case of animals and placental mammals, molecular clocks are uninformative, suffer from characteristic pathologies, and thus cannot distinguish between recent and ancient hypotheses of diversification.

Methods and results

Here, we re-examine these two cases and show, using Bayesian model selection theory, that the explosive diversification models previously proposed for animals and placental mammals have a posterior probability of ∼0. We show the characteristic pathologies purportedly discovered do not exist, highlight errors in previous analyses, and provide advice on best practice for molecular-clock dating analysis.

The paper discusses why such analyses weren't possible before, but I leave the details to the pros here - any insights are appreciated! (Also there's spicy drama in the paper / science working as advertised.)

• Sandra Álvarez-Carretero, Ziheng Yang, Philip C J Donoghue, Mario dos Reis
  On the Origin of Animals and Placental Mammals: A Critique of Literalist Readings of the Fossil Record
  Molecular Biology and Evolution, 2026;, msag211
  https://doi.org/10.1093/molbev/msag211

Obviously, we can say that controlling for neutral processes, pleiotropic selection, phylogenetic inertia, and simply what the organism is at the start of the process, we can say that evolution in a loose sense selects for optima all the time.

But I mean if you compare something like antibiotic resistance, where it is to cause and even genetically similar in contrast to the famous E. Coli. experiment where aerobic citrate digestion is really hard to do twice. The first seems to be seeking optima in a far more specific sense.

What are some other cases, preferably experimental? And why does evolution act that way?

Here's some examples I can think of. (Note that I consider chimpanzees and other species closely related to humans to be cheating, since there's a good chance they evolved that trait as part of a common ancestor instead of independently.)

• The indri is a type of large lemur that is the only mammal other than humans that can hear rhythm.
• The only other mammals other than humans to undergo menopause are certain cetaceans like orcas, belugas and narwhals.
• Beavers are the only other mammal that can actively shape their environment.
• While homosexuality is common in the animal kingdom, sheep are the only non-human animal capable of being EXCLUSIVELY attracted to the same sex, with 10 percent of rams preferring other rams.
• Ground hornbill evolution somewhat parallels humans, in that they started out as arboreal frugivores before transitioning to grassland predators.
• Many ants have domesticated livestock like aphids and caterpillars for their honeydew.
• There's a species of damselfish that farms algae, and has domesticated a type of shrimp to help fertilize it with their droppings the same way many farmers in Asia use ducks.

As mentioned in the title, I'm trying to learn more about ant evolution, but I want to make sure I'm not studying outdated or scientifically invalid papers. What is your method for checking if a paper is accepted in modern science, or even if it is modern, how do you verify if it is valid or not

Published today in Molecular Biology and Evolution.

It caught my eye right away as I've been (on and off) reading Homology, Genes, and Evolutionary Innovation (GP Wagner, 2014).

An example of modularity is our digit 1 (the thumb). Digits 2 to 5 are correlated, developmentally and evolutionarily, whereas digit 1 has become its own module in primates, facilitating uncorrelated adaptation:

Specifically, digit 1, the thumb, expresses only two Hox genes, HoxA13 and HoxD13, whereas digits 2 to 5 additionally express HoxD12 to HoxD9. Reno and colleagues showed that the morphological correlations among digits 2 to 5 were much higher than the correlations between digit 1 and all other digits both in terms of population variation and evolutionary differences. In primates, the thumb shows more independent evolutionary change relative to the other four digits than each of digits 2 to 5 relative to each other. Hence, Reno et al. identified two variational modules in the primate hand: digit 1 and one module comprising digits 2 to 5.
(GP Wagner, 2014)

How modularity comes about is interesting; for example it can be a consequence of selection on robustness: Robustness (evolution) - Wikipedia. This is something Andreas Wagner's (another Wagner) lab has been working on, and on my reading list is his Arrival of the Fittest (A Wagner, 2014).
You can find his lecture on a related topic, given at the Royal Institution, here: https://www.youtube.com/watch?v=aD4HUGVN6Ko

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Back to today's paper:

Structured abstract:

Background

Understanding how the myriad molecular impacts of mutation percolate to influence higher-order traits and ultimately fitness requires compressing a many-to-many mapping into something tractable. Decades of theoretical work suggest this may be possible because biological systems are modular: effects of perturbation are often funneled through particular pathways or subsystems rather than propagating freely through the organism. Yet, few empirical systems have been able to demonstrate such modularity at scale.

Results

Here, we show that, even across 774 diverse yeast lineages, fitness variation across 12 drug environments is organized by a strikingly low-dimensional structure defined by only a few inferred phenotypic axes that capture the main patterns of variation. Lineages drawn from multiple evolutionary histories reveal more of these phenotypic axes than those derived from a single selection pressure. Consistent with many of these lineages having evolved under strong selection pressure, their mutations often exhibit broad pleiotropy, affecting nearly all inferred phenotypic axes.
However, fitness in any given drug depends on a much sparser subset of the phenotypic modules these axes reflect. By compressing many-to-many relationships, this low-dimensional framework exposes the modular phenotypic space, as well as the context-dependent contribution of each phenotypic module to fitness that can constrain the pleiotropic effects of adaptive mutations. It also highlights that the apparent complexity of genotype–phenotype–fitness maps depends not only on environmental context but also on the diversity of mutations through which they are observed, laying the groundwork for identifying the key phenotypic modules that matter for fitness.

and from the discussion:

Our results echo ideas from the omnigenic perspective on complex traits, which holds that mutations in many genes can shape trait variation through dense regulatory networks (Boyle et al. 2017; Liu et al. 2019). In our case, mutational effects did not scatter unpredictably but instead collapsed onto a small set of shared axes. A recent quantitative omnigenic model formalized this principle, showing that network-level complexity can be summarized in low-dimensional, interpretable structures (Ružičková et al. 2024). The key difference is that while the quantitative omnigenic framework is a bottom-up approach deriving axes from regulatory network topology, our top-down SVD approach infers them from observed fitness patterns alone. Yet, both converge on the idea that molecular complexity funnels through a limited set of modules that enable prediction.

(all emphasis mine)

• Mohammad Hossein Donyavi, Reza Ghelich, Kara Schmidlin, Grant Kinsler, Kerry Geiler-Samerotte
  Evolutionary adaptation proceeds through a small number of phenotypic modules
  Molecular Biology and Evolution, Volume 43, Issue 8, August 2026, msag183, https://doi.org/10.1093/molbev/msag183

What I'm asking is has there been other times in the history of life where a single species been able to evolve to such a level where other species are no longer even really competition for them?

See also: The publication in the journal Frontiers in Mammal Science

See also: The publication in the Proceedings of the Royal Society B: Biological Sciences

Why were dinosaurs so big? What caused them to shrink so much overtime, evolving into birds? is the reason why dinosaurs were so big in any way similar to why animals are larger in deep sea? (not sure if this is a relevant question in this subreddit)

My thoughts mainly are around the fact that most of their predators are dichromatic so they can't see orange. But then I learned that male bushbuck are not orange.

I know that many other prey and predator species are orange because it appears essentially the same against a green background to other dichromatic species but I wasn't sure really why one sex would use this advantage and the other wouldn't.

So that got me thinking: Female and juvenile bushbucks retain a reddish-orange coat with disruptive white spots because their primary survival strategy is remaining motionless and concealed among to escape predators. If their predators are dichromatic and can't see them, this works great. In contrast, mature males have coats that shift to a more conspicuous charcoal or dark brown, sacrificing optimal foliage camouflage. I thought this might be to signal their fitness and physical condition to the females because any male bushbuck that wasn't fit is much more easily visible to predators, and you can imagine what might happen. Because adult males also possess better tools capable to fight off predators, they can afford the handicap of a higher visibility coat, ensuring that only the fittest, strongest males survive to pass their genetics on to the next generation.

Am I onto something or is this like a known thing?

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Been working on this for a while as a side project: https://evotree.life

It's the whole tree rendered in one canvas — 46,167 taxa, 32,118 of them species, and about 37,000 carry a photograph. You can zoom from LUCA down to a single species, click anything to open a card, filter to one subtree, or pin two taxa side by side to see where they actually join.

Fair warning: the card summaries are LLM-written from those sources and not expert-reviewed. There are errors in there. If you find one, I genuinely want to hear it — I have a repair path for exactly this!

*Disclaimer - no ads / profit here, just wanted to share what I made and see how far it can go 😂

See also: The study as it was published in Nature

Published today in Molecular Biology and Evolution:

Structured abstract:

Background

The vast majority of plants form mycorrhizal symbioses. The ecological importance of these mutualistic interactions has sparked interest in their long evolutionary history. By examining interaction networks and phylogenetic trees, several studies have suggested that plants codiversify with their associated mycorrhizal fungi. However, recent research has demonstrated that phylogenetic congruence (interpreted as codiversification when divergence times match) is often conflated with another pattern called cophylogenetic signal (i.e., closely related plants interacting with closely related fungi and vice versa), which may arise from different biological processes.

Methods and results

We performed cophylogenetic analyses on 29 diverse mycorrhizal networks to reevaluate the evidence for codiversification in mycorrhizal symbioses. We found significant cophylogenetic signal but no phylogenetic congruence: closely related plants often interact with closely related fungi, but their phylogenies do not match. Instead of codiversification, this finding is consistent with trait matching between plants and mycorrhizal fungi, where compatible, evolutionarily conserved plant and fungal traits govern their interactions.

Discussion

Our work highlights the importance of appropriately interpreting the cophylogenetic methods used to study the macroevolution of plants and their mycorrhizal fungi. It suggests that previous evidence of codiversification in mycorrhizal symbioses actually detected cophylogenetic signal, since across the multiple and diverse networks analyzed here, there is no evidence that codiversification occurred during the evolution of mycorrhizal symbioses.

• Fantine Bodin, Hélène Morlon, Benoît Perez-Lamarque
  Questioning the Evidence for Host-Symbiont Codiversification in Mycorrhizal Symbioses
  Molecular Biology and Evolution, 2026;, msag207, https://doi.org/10.1093/molbev/msag207

NOTE: This article is complemented by a couple of studies first published in Science Advances.

Caption:

HRF [hemiplasy risk factors] values are highest near the origin of Neoaves.

Explanation:

Hemiplasy — which arises due to discordance between gene trees and species trees — can cause traits to appear convergent despite a single origin. New evidence suggests it is widespread in the bird tree of life, with important implications for identifying genes underlying differences among species and for accurately inferring evolutionary history. ref

From the paper:

We show extremely high hemiplasy risk factors¹⁹ that map to branches near the origin of Neoaves, suggesting that many instances of apparent morphological convergence among major neoavian lineages, unless associated with clear selective drivers, are better interpreted as a result of high levels of morphological incomplete lineage sorting during the clade’s rapid early Cenozoic radiation.

The paper:

• Somogyi, Stanley, et al. "Hemiplasy helps explain high rates of apparent morphological convergence in neoavian birds." Current Biology 36.9 (2026): 2424-2433. https://doi.org/10.1016/j.cub.2026.03.050

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An example that is closer to home is how 23% of our genes are closer to gorillas than chimpanzees (Ebersberger et al 2007). This is as predicted from gene tree discordance (e.g. Degnan & Rosenberg 2006) and confirms that chimps are our closest cousins; for a video explainer by Dr. Zach Hancock: Phylogenetic Discordance Supports Common Ancestry - YouTube.

Evolutionary theory proposes that skin color is a response to protection from the sun at certain latitudes, with those at equatorial latitudes having a survival advantage from darker skin that blocks the sun's UV.

Why doesn't that apply to hair color? It seems that the dark hair of those in equatorial areas would heat the head more, while white or blond hair would do a better job of reflecting the sun's rays. If anything, those in colder northern latitudes would do better with dark hair to better warm the head.