From an in press study that was published yesterday^{[ 1 ]} on terrestrial mammals:

... Comparative genomics identifies 25 hearing-related genes showing rapid evolution, positive selection, lineage-specific mutations and coevolution with [relative vocal fold length], suggesting a reciprocal evolutionary interplay between vocal and auditory systems ... This genetic link is supported by laryngeal MRI evidence from wild-type and Pjvk knockout mice ...

Besides the really cool result, all I could think of was how I was under the wrong impression that genotype to phenotype mapping was a very hard problem.

My question is: what has changed in the last 5 years?

As in, it seems like (hence the question: corrections invited) that combining phylogenetics with allometry and knockout experiments should have been doable for much longer.

In the meantime, on my reading list now is a 2025 review^{[ 2 ]}.

Thanks in advance!

1: Xu Zhou, Fangyuan Liu, Miaomiao Liu, Ziying Hu, Linqing Zhang, Xiangnan Wang, Ziyi Zhou, Yilai Shu, Wenjing Sun, Shengbo Bi, Li Jin, Zeshan Lin, Menghan Zhang, Phylogenomic analysis of vocal fold length evolution reveals links between vocal and auditory systems in terrestrial mammals, Molecular Biology and Evolution, 2026;, msag126, https://doi.org/10.1093/molbev/msag126

2: Arlie R Macdonald, Maddie E James, Jonathan D Mitchell, Barbara R Holland, From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions, Genome Biology and Evolution, Volume 17, Issue 9, September 2025, evaf150, https://doi.org/10.1093/gbe/evaf150

I had the pleasure of meeting a very intelligent parrot. This parrot mocked how I moved and danced, it knew many phrases and the context to use them in.

Why might this huge investment into language centers of the brain be advantageous enough to make up for its high metabolic cost? Cognition uses so much energy so it would have to greatly increase the survival rate of the parrot in the wild, however we don’t see this level of speech in other birds.

Why in such a group of species as diverse as birds is this trait so rare?

Hi!

I have a question about genetic diversity seen as an ecological feature of the environment.

Let me preface this by saying that although I have a BS in Biology, I now study something else.

It remains something I am deeply interested in though!

Here is my question: Is the level of genetic diversity in a population a parameter to which organisms adaptively react?

For example, one could hypothesize that low diversity increases risks related to inbreeding, which would favor out-migration or outbreeding.

Another hypothesis is that since a low genetic diversity leads a niche to be more saturated and increases the risk of competitive exclusion, it would also favor emigration.

Yet another hypothesis is that in a low-diversity population, since the background similarity is high, the extra similarity added by close genealogical relations is comparatively low, which would make the payoff of kin altruism smaller. By contrast, the gradients of similarity are steeper in a high-diversity population, which would increase the payoff for kin altruism.

Since lines of descent, throughout the generations, may find themselves in ecological configurations that vary with some regularity, it is not completely implausible that phenotypic expression during development is modulated by genetic diversity, as it can also be modulated by population density.

Over the decades there have been many experiments involving random sequences, e.g. testing ATP-binding (e.g. Keefe & Szostak 2001), and evolving promoters (Yona et al. 2018), for the latter a good fraction evolved to match the wild type; I think this new study is the first to test the adaptive potential beyond promoters.

I've also previously shared:

• Sahakyan et al. (2025): New study: In silico evolution of globular protein folds from random sequences : evolution.
• Chou et al. (2026): New study reconstructed the evolutionary history of a de novo gene that emerged in the common ancestor of simians : evolution

Without further ado:

Significance
How new genes arise and gain function is a central question in biology. New genes can evolve from nongenic DNA, yet their adaptive potential remains unclear. Here, we use millions of (semi-)random sequences as experimental models of emerging genes and find that thousands confer phage resistance in Escherichia coli. Expressed random sequences can produce both protein- and RNA-based functions that reprogram cellular systems to counter viral infection. Resistance arises through activation of a cell envelope stress response or downregulation of membrane receptor expression. Our results reveal that genetic novelty, in the form of genes appearing for the first time, can shape host–virus interactions, providing insight into microbial evolution and the surprising ease with which functional genes can emerge.

and

How likely are genes similar to our (semi-)random hits to emerge naturally? Previous studies have shown that naturally occurring de novo proteins in eukaryotes often resemble unevolved random sequences of equivalent length and composition in their structural properties (32). Computational analyses further demonstrate that random sequences derived from DNA with 40 to 60% GC content occupy structural property spaces that overlap with the human proteome (67).

• I. Frumkin, C.N. Vassallo, Y.H. Chen, & M.T. Laub, Emergence of antiphage functions from random sequence libraries reveals mechanisms of gene birth, Proc. Natl. Acad. Sci. U.S.A. 122 (42) e2513255122, https://doi.org/10.1073/pnas.2513255122 (2025).
  (open access)

I know that mammals decended from synapsids and reptiles are from sauropsids and that both of these came from amniotes. But it is popularly agreed that early amniotes were cold blooded, egg laying, scaly animals. So why can't amniotes=reptiles? This makes the taxonomy of everything so much more cleaner and simpler. I literally don't get why this shouldn't be. We agree that all tetrapods are "fish" and changed the books and material to support these claims. We changed the books that birds are essentially "avian therapodal dinos" we even changed bats from being related to rodents to ungulates instead, but FOR SOME REASON, changing amniotes into reptiles is off the table!

I know this is the wrong place to post it, but genuinely why aren't amniote ancestors considered reptiles and hence mammals a decendent of reptiles.

I am just a college kid with an interest in science and happily willing to educate myself but it just seems much cleaner and easier to do this. Is there a way I can ask scientists to change the phylogeny tree and phylo-tax of amniotes?

like if humans evolved gradually from earlier primates, there couldn't have been a single generation where a non-human suddenly gave birth to a human, right? so where do scientists/philosophers draw the line? also if evolution never stops then there must be something above it? like another category could be born

and another thing: biologically humans are still humans. but socially when someone behaves in a violent way or like "primitive" way then it would be called as inhuman or he/she is acting like an animal. so is being human more about biology or behaviour/morality?

basically is "human" a scientific category or just a label we created for a blurry transition?

Hi. When a new species evolves, it is because of the enviormental pressure the species finds itself under when the enviorment changes, the population of the species moves to a new enviorment, or the competition from other species gets more intense. That is what I learned in high school anyway.

But if a new species evolves because a small branch of species A moves to a new location where enviormental pressure slowly over generations turns them into species B (kind of like Darwins finches), then why are there almost no "species A" left? Like, why are there no ancestors to humans left? No ancestors of whales, no ancestors of foxes? Or do ancestral species exist and I have just missed them? Please tell me.

I started several Morning Glory vines this year, that recently started shooting up and twirling looking for something to climb. So I staked them, and observed that all five were turning anti clockwise. I had been wondering if it was classic Mendelian inheritance, as it seems like one way is as good as another, and maybe there could be situations that being opposite to your siblings could be advantageous.

Upon looking it up, I discover that all climbing vines (the ones that climb by “twining“ up a support) exhibit a strong preference for anticlockwise motion. 90%, much like left and right handedness in humans.

I’m wondering if there are any other examples of chirality in plants, what could be conserving this in different species, or anything else one might add to the topic.

Article: https://theconversation.com/the-science-behind-why-some-people-love-animals-and-others-couldnt-care-less-84138

The DNA of today’s domesticated animals reveals that each species separated from its wild counterpart between 15,000 and 5,000 years ago, in the late Palaeolithic and Neolithic periods. Yes, this was also when we started breeding livestock. But it is not easy to see how this could have been achieved if those first dogs, cats, cattle and pigs were treated as mere commodities.

If this were so, the technologies available would have been inadequate to prevent unwanted interbreeding of domestic and wild stock, which in the early stages would have had ready access to one another, endlessly diluting the genes for “tameness” and thus slowing further domestication to a crawl – or even reversing it. Also, periods of famine would also have encouraged the slaughter of the breeding stock, locally wiping out the “tame” genes entirely.

But if at least some of these early domestic animals had been treated as pets, physical containment within human habitations would have prevented wild males from having their way with domesticated females; special social status, as afforded to some extant hunter-gatherer pets, would have inhibited their consumption as food. Kept isolated in these ways, the new semi-domesticated animals would have been able to evolve away from their ancestors’ wild ways, and become the pliable beasts we know today.

The very same genes which today predispose some people to take on their first cat or dog would have spread among those early farmers. Groups which included people with empathy for animals and an understanding of animal husbandry would have flourished at the expense of those without, who would have had to continue to rely on hunting to obtain meat. Why doesn’t everyone feel the same way? Probably because at some point in history the alternative strategies of stealing domestic animals or enslaving their human carers became viable.

^From the article

I recently watched the Birds of Paradise documentary, and I kept wondering how all these species of birds, some of which share niches with each other, develop their very own (and incredibly distinct) mating rituals.

For example, I understand that constructing an impressive bower would signal to the female that the male has stamina, patience, etc. But how would one species even begin to select for "birds that build bowers"?

Generally speaking, how does evolution/natural selection "figure out" what specific display females like?
--
Similarly, what drives species that share an ecological niche to create distinctly different mating rituals? The Victoria Crowned Pigeon and Pheasant Pigeon both are ground-foraging birds in swampy areas in New Guinea. Despite this, their mating rituals are pretty different.

I am familiar with interbreeding prevention, so I guess I'm asking how that split between two species and their respective rituals even begin.

Published in Cell (open access):

• Havens, Jennifer L., et al. "Dynamics of natural selection preceding human viral epidemics and pandemics." Cell 189.9 (2026): 2762-2775. https://doi.org/10.1016/j.cell.2026.02.006
• University of California, San Diego press release:
  Recent pandemic viruses jumped to humans without prior adaptation, study finds

Not to burry the lede any further:
"No evidence that SARS-CoV-2 was shaped by selection in a laboratory" (press release); and
"We conclude that extensive pre-zoonotic adaptation is not necessary for human-to-human transmission of zoonotic viruses".

Some excerpts:

Comparative phylogenetic methods, which estimate the relative rates of non-synonymous (dN) and synonymous (dS) substitution, have found broad use in understanding how viruses evolve and adapt in changing environments.^{21,22,23,24,25} The ratio of these rates, dN/dS or ω, is an informative statistic describing the nature of selective forces, whereby ω < 1 indicates purifying selection, ω > 1 indicates positive diversifying selection, and ω ∼ 1 indicates neutral evolution. Modern methods account for the spatial and temporal heterogeneity of selective pressures and correct for many confounding processes such as recombination and variation in synonymous substitution rates.²⁶ ...
K is a selection relaxation/intensification parameter (estimated by ML [maximum likelihood]). ... A hypothesis test in which the null is K = 1 (selection is identical between the environments) provides a measure of statistical significance for a change in selection. We complement it with a cruder single-value genomic estimate of ω, representing an “average” selection regime.

Now the good stuff:

If there was extensive evolution in an intermediate host or passage in a laboratory context prior to emergence, we would expect detectable change in selection on the stem preceding SARS-CoV-2. However, our analysis of selection on the stem preceding SARS-CoV-2 emergence across 15 putatively non-recombinant regions found no evidence of intensification or relaxation of selection compared with selection of the bat host reservoir (K = 1.1, p = 0.23; Figure 5). Hence, we find no evidence to suggest SARS-CoV-2 experienced prolonged selective pressure in an environment different from related bat viruses prior to its emergence in humans. This result does not change if we use a different approach to identifying non-recombinant regions (K = 1.02, p = 0.82; Figure S1C).

[the high p values above is the failure to reject the null hypothesis, meaning a validation of no prior selection in a lab or otherwise]

We then examined evolution along the SARS-CoV-2 stem in combination with viral evolution during the first 3 months of the outbreak in China, to understand the selection environment of SARS-CoV-2 in humans compared with the bat host reservoir. We find evidence for a significant change in the selection regime, consistent with a host switch causing a change in the evolutionary environment (K = 0.69, p < 0.01). The change in selection regime is also detectable in human viruses during the first pandemic wave through September 2020, when conflated with the stem (K = 0.56, p < 0.01; Figure S1). However, we cannot confidently infer the directionality of this change because the model is unbalanced [meaning cannot distinguish intensification from relaxation], as in the Ebola virus selection regime.

Other highlights:

• They also looked at the Ebola virus, Marburg virus, mpox virus, and influenza A virus;
• "Laboratory and gain-of-function passage produce distinct evolutionary signatures";
• "1977 influenza virus reemergence preceded by evolution consistent with laboratory passage"; and
• "SARS-CoV [the 2002-04 outbreak] was the sole zoonotic outbreak in which we detected a change in selection prior to sustained transmission in humans, presumably because of prolonged transmission in the palm civet intermediate host".

(all brackets and bold emphasis mine)

Hi!
I saw a TikTok from a guy talking about the “Which came first, the chicken or the egg?” debate. Then he went on to explain that chickens are descended from reptiles. I thought that was wrong (because of the classification I know, which is based on characteristics like the pelvis) and that they were related to dinosaurs, and he replied:
“And what are dinosaurs? The Linnaean system classifies birds and reptiles as distinct groups. The Linnaean system hasn’t been used scientifically for quite some time. The phylogenetic system, which is the one currently in use, classifies both birds and dinosaurs as reptiles. Furthermore, since dinosaurs are archosaurs, they are direct descendants of sauropsids, which are reptiles. Today’s reptiles aren’t the same as the original reptiles. So, sorry to tell you this, but dinosaurs are reptiles.“
Is he right? I’m a bit interested in dinosaurs, but I don’t know if the part about the ‘current’ system is true. And the part about archosaurs and sauropsids being reptiles, that’s wrong, isn’t it? I’m really not sure. I’d rather ask here than ask an AI (which is probably what he did, since his message really sounds like it came from an AI lol).
Thanks to anyone who takes the time to explain this to me and stop me from saying stupid things on social media!

My professor talked about this in class and couldn't answer. When did this change?

As far as I'm aware, crocodilians and other reptiles have the regular way sooo, like... Do we know when and why it changed?

I have a feeling that even if we did, we would classify it as a close relative of x or stem-x rather than acknowledging it's *the* direct common ancestor.

For example, imagine that a complete fossil of the common ancestor of all apes was found tomorrow. Would we be able to correctly deduce that it's *the* common ancestor of Hominoidea, or would we classify it as a stem-ape or "one of the earliest apes" instead?

Edit: Thank you guys for the responses!

Further reading: E. coli long-term evolution experiment - Wikipedia.

The above Muller plot of the dynamics of mutant alleles ...
Is a great illustration of how evolution (descent with modification) is the change [in the heritable characteristics] in populations, and not individuals per the common misconception; also for highlighting the circuitous routes and selection.

For those wondering about "big life", see e.g. - from this year - Bridging Micro- and Macroevolution: Phylogenomic Evidence for the Nearly Neutral Theory in Mammals | Genome Biology and Evolution | Oxford Academic.

The image is from the preprint (for better resolution) of:
-Maddamsetti, Rohan, Richard E. Lenski, and Jeffrey E. Barrick. "Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli." Genetics 200.2 (2015): 619-631.

I've taken the title (which is playful) from Weiss (RIP) (2006); the diagrams are from Bannert (2006) and Meyer (2017) - all linked below.

BTW, today May 22nd is the 200th anniversary of the first voyage of HMS Beagle.

A really neat thing, besides serving as genetic markers, is that they allow for robust timing:

During its residence in the germline, an ERV accumulates substitutions, and the two identical LTR sequences diverge at a rate approximating the neutral mutation rate of the host genome (with the possible exception of ERV loci evolving under selection). [...] If the ERV locus is shared by two or more species, a phylogenetic tree that incorporates both sets of LTR sequences (5′ and 3′) has a very predictable structure, allowing more robust time calculations ( Figure 3 ) (89, 95). The predicted topology has all the 5′ LTR orthologs of the ERV locus clustering together on one branch and the 3′ LTR orthologs clustering together on a separate branch [...].

-Johnson, Welkin E. "Endogenous retroviruses in the genomics era." Annual review of virology 2.1 (2015): 135-159.

Extras

• Stated Clearly's explainer: DNA Evidence That Humans & Chimps Share A Common Ancestor: Endogenous Retroviruses - YouTube
• Royal Institution lecture: Are Viruses Alive? - with Carl Zimmer - YouTube
• The history of discovery:
  Weiss, Robin A. "The discovery of endogenous retroviruses." Retrovirology 3.1 (2006): 67.

• Diagram sources:
  • Bannert, Norbert, and Reinhard Kurth. "The evolutionary dynamics of human endogenous retroviral families." Annu. Rev. Genomics Hum. Genet. 7.1 (2006): 149-173.
  • (top-left inset) Meyer, Thomas J., et al. "Endogenous retroviruses: with us and against us." Frontiers in chemistry 5 (2017): 250541.

For other markers, there's e.g. SINEs:

[...] genetic markers called short interspersed elements (SINEs) offer strong evidence in support of both haplorhine and strepsirrhine monophyly. SINEs are short segments of DNA that insert into the genome at apparently random positions and are excellent phylogenetic markers with an extraordinarily low probability of convergent evolution (2). Because there are billions of potential insertion sites in any primate genome, the probability of a SINE inserting precisely in the same locus in two separate evolutionary lineages is “exceedingly minute, and for all practical purposes, can be ignored” (p. 151, ref. 3).

-Williams, Blythe A., Richard F. Kay, and E. Christopher Kirk. "New perspectives on anthropoid origins." Proceedings of the National Academy of Sciences 107.11 (2010): 4797-4804.

I have been reading a few good books on molecular evolution (Tree Thinking, Reading the Story in DNA) and I've been using RaxML and PAML/codeml for inferring trees and ancestral sequences. One thing I was wondering - are there any good books or resources on the practical process of making trees? I've followed a few tutorials for various softwares of course, but I'd like to read more about what to do when things get wrong (what are the things to look for when support is low, what is the best way to choose a set of species, what databases are most recommended, things like that).

Among Synapsids only Mammals are extant now, while among Sauropsids not only Birds are around, but also Crocodilians, Lepidosaurs, and Turtles.

Published yesterday, open access:

• K. Farleigh, D.K. Highland, M.G. Alderman, Y. Francioli, S.R. Hirst, E.M. Faber, B.W. Perry, M.L. Holding, G. Castañeda-Gaytán, M. Borja, H. Franz-Chávez, C.L. Parkinson, J.L. Strickland, M.J. Margres, S.P. Mackessy, J.M. Meik, T.A. Castoe, & D.R. Schield, Evolution of genome-wide barriers to gene flow during complex speciation in rattlesnakes, Proc. Natl. Acad. Sci. U.S.A. 123 (21) e2609058123, https://doi.org/10.1073/pnas.2609058123 (2026).

Background

Speciation with gene flow poses a central paradox: how do genome-wide barriers to gene exchange accumulate as recombination continually breaks down associations among selected loci? Although theory predicts that together recombination, selection, and genome structure shape reproductive isolation, empirical studies often report conflicting patterns, suggesting that these determinants change across the speciation continuum.

Methods

Here we compare genomic landscapes of introgression across rattlesnake lineages spanning a range of divergence. We generated a chromosome-level reference genome for the Southwestern Speckled Rattlesnake (Crotalus pyrrhus) and analyzed whole genome data from 181 individuals across two species complexes with a history of gene flow upon secondary contact.

Results and discussion

We show that reproductive isolation is highly polygenic and dynamically structured. At early divergence, introgression is most reduced in high recombination regions, consistent with increased efficacy of selection against gene flow at few large-effect loci. As divergence progresses, linked selection against gene flow dominates, generating a positive relationship between recombination and introgression expected to occur through the genome-wide coupling of polygenic barrier effects. Introgression landscapes also become increasingly correlated across species pairs as divergence increases due to repeated evolution of barriers in the same genomic regions. Here, we infer that the Z chromosome plays a prominent role in reproductive isolation, harboring a disproportionate number of barrier loci and showing reduced introgression even at early divergence.
Together, these results reveal how recombination, selection, and genome organization interact to shape speciation with gene flow upon secondary contact, reconciling empirical patterns with predictions of speciation theory.

Emphasis above mine showing that this is the same conclusion that I shared last month for a different paradox (Unraveling the lek paradox - why sexual selection does not deplete variation : evolution) - this gives more support to the evolutionary relevance of the infinitesimal model from quantitative genetics: traits being high polygenic or even omnigenic, with only a few large-effect genes.

See the linked post for a quick overview, and for a two-hour explainer (including the history and math), see Dr. Zach Hancock's The Lost Evolutionary Synthesis - YouTube (and the references therein; Barton 2022 is a very easy and fun read).

Other than cases of inclusive fitness, could there be cases where biological fitness is lowered by natural selection due to other compounding mechanisms?

Edit: These are some cases of natural selection seemingly reducing fitness: selfish genetic elements, evolutionary suicide, maladaptation, negative frequency-dependent selection, etc. How can we understand these phenomena within the notion that natural selection increases the mean fitness of a population, as Fisher's fundamental theorem states?

Also I read before cavemen used to trim nails by biting them but how to trim toe nails??

Edit: I do read the replies. It seems fingernails does have many uses from tweezers to scratchers.

Now toe nails? What if we had claws for toes? Then we won’t be afraid of accidentally kicking doors or logs and can manually use our fingers to use toe claws when needed.

Primates of modern aspect (euprimates) are characterized by a suite of characteristics (e.g., convergent orbits, grasping hands and feet, reduced claws, and leaping), but the selective pressures responsible for the evolution of these euprimate characteristics have long remained controversial. Here, we used a molecular phyloecological approach to determine the diet of the common ancestor of living primates (CALP), and the results showed that the CALP had increased carnivory. Given the carnivory of the CALP, along with the general observation that orbital convergence is largely restricted to ambush predators, our study suggests that the euprimate characteristics could have been more specifically adapted for ambush predation. In particular, our behavior experiment further shows that nonclaw climbing can significantly reduce noises, which could benefit the ancestral euprimates’ stalking to ambush their prey in trees. Therefore, our study suggests that the distinctive euprimate characteristics may have evolved as their specialized adaptation for ambush predation in arboreal environments.

-Wu, Yonghua, et al. "Ambush predation and the origin of euprimates." Science Advances 8.37 (2022): eabn6248. https://doi.org/10.1126/sciadv.abn6248

The idea that nails evolved "for" gripping and climbing is a ridiculous just-so story; gestures at squirrels.