#phylogenetic analysis

[mdnewsline1]

Discover Hidden HIV Transmission Patterns: A Breakthrough Study

Learn how advanced molecular analysis is uncovering concealed transmission routes of HIV-1 F1 subtype in Romania. This study highlights the discrepancies between self-reported data and actual transmission networks, particularly among MSM (Men who have Sex with Men) and PWIDs (People Who Inject Drugs).

Key Highlights:

Larger transmission clusters among MSM than self-reports reveal.

Overrepresentation of heterosexual transmission in self-reported data.

Molecular tools like FastTree and ClusterPicker identify 25 distinct clusters.

Revolutionize HIV prevention efforts with insights from this critical research.

Read More: https://mdnewsline.com/tracking-transmission-routes-in-romanian-hiv-1-f1-subtype/

Empowering public health with science!

[agent-oo-z]

Fun fact about me! Ya know that famous bird video meme? The “bitches love blue” and “lemme smash” one? The first time I saw it my reaction was “oh I know that bird! That’s a bower bird! The males build these complex structures and then decorate them to attract mates!”

Which is true, it’s very cool and interesting. But I was so caught up in the autism moment of “I can identify this animal and I know about its behavior” that when the voice over started talking about Ron and Becky and Ben I fully lost my shit because I had only been half processing the words up until that point.

Anyways I am so very autistic and I just. Know things. About animals. Like it’s my whole bit.

[todays-xkcd]

There's a maximum likelihood that I'm doing phylogenetics wrong.

Geometriphylogenetics [Explained]

Transcript

[A tree diagram, or a dendrogram is shown, consisting of lines that branch off from left to right, starting with one horizontal line on the left. Eight results are shown on the right: ellipse on Path 1, circle on Path 2, triangle on Path 3, parallelogram on Path 4, trapezoid on Path 5, square on Path 6, rectangle on Path 7, and a pentagon on Path 8. The paths are listed in order top to bottom.] [Path 3 and the triangle are bold black, while the other branches are dimmer. The paths are connected as follows: Path 2 and 3 are connected, then both connect together to Path 1; Path 4 and 5 are connected, as are Path 6 and 7, and these two paths are connected altogether; Path 8 is then connected to the branch containing Paths 4 to 7. All of Paths 1 to 3 are then connected to Paths 4 to 8, the branches all culminating in a single line on the left.] [Caption below the panel:] The phylogenetic revolution continues: Triangles were long believed to be related to squares, but genetic analysis proves that they are actually very pointy circles.

[herpsandbirds]

A remarkable new blue Ranitomeya species (Anura: Dendrobatidae) with copper metallic legs from open forests of Juruá River Basin, Amazonia

Esteban Diego Koch, Alexander Tamanini Monico, et al.

ABSTRACT

Poison dart frogs (Dendrobatidae) are known for their aposematic coloration and toxic skin, making them a frequent subject of interest and research. However, descriptions of new species of Ranitomeya were interrupted for more than a decade. The implementation of a RAPELD (Rapid Assessment surveys of Long-Term Ecological Research) module in the Juruá River basin, a highly biodiverse and underexplored region, led to the record of a Ranitomeya species with blue dorsal stripes and coppery limbs. Herein we use morphological, morphometric, advertisement call, natural history, tadpole data and genetic data to describe the new species. Our phylogenetic analysis places the species within the Ranitomeya vanzolinii clade, and all delimitation methods confirmed its status as a new species. The species is characterized by its (i) small size (snout-vent length: males 15.2–17.0 mm, females 14.4–16.9 mm), (ii) dorsum with light sky-blue stripes on a reddish-brown ground, and metallic copper limbs with reddish-brown spots, (iii) ring-shaped granular region on the belly, (iv) toes with poorly developed lateral fringes, (v) later tadpole stages with tooth rows P1 = P2 > P3, P3 of 83–87% of P1, and conspicuous light sky-blue dorsal stripes, and (vi) cricket-like advertisement call consisting of 16–35 notes, call duration of 490–1,005 ms, note duration of 8.2–16.9 ms and dominant frequency of 5,168–6,029 Hz. The discovery of the new species emphasizes the significance of researching under-sampled regions like the Juruá River basin, and the usefulness of using a multidisciplinary approach to reveal new dendrobatid species.

Read the paper here:

A remarkable new blue Ranitomeya species (Anura: Dendrobatidae) with copper metallic legs from open forests of Juruá River Basin, Amazonia | PLOS One

[alphynix]

Miosiren kocki was a sirenian (sea cow) that lived during the early Miocene (~20-15 million years ago) in what is now the North Sea basin in northwestern Europe.

Similar in size to the very largest modern manatees, about 4-4.5m long (~13-14'10"), it has traditionally been classified as an early member of the manatee lineage – but a study in 2022 suggested it may instead represent a much earlier stem of the sirenian evolutionary tree, with its ancestors potentially having diverged around 34 million years ago.

It had unusually thickened bones in its skull, especially around the roof of its mouth, which would have given its jaws a very strong chewing force. Isotope analysis of its teeth show it was part of a marine algae-based food web, unlike the seagrass-based diets of other sirenians, so it may have been specialized to feed on a much tougher diet. Possibly it was eating something like calcareous algae, or more speculatively it might even have been crunching on hard-shelled algae-consuming marine invertebrates.

———

NixIllustration.com | Tumblr | Patreon

References:

Clementz, Mark T., Silvia Sorbi, and Daryl P. Domning. "Evidence of Cenozoic environmental and ecological change from stable isotope analysis of sirenian remains from the Tethys-Mediterranean region." Geology 37.4 (2009): 307-310. https://doi.org/10.1130/G25533A.1

Domning, Daryl P. "What Can We Infer About the Behavior of Extinct Sirenians?." Ethology and behavioral ecology of Sirenia. Cham: Springer International Publishing, 2022. 1-17. https://doi.org/10.1007/978-3-030-90742-6_1

Heritage, Steven, and Erik R. Seiffert. "Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria)." PeerJ 10 (2022): e13886. https://doi.org/10.7717/peerj.13886

Wikipedia contributors. “Miosiren” Wikipedia, 18 Nov. 2024, https://en.wikipedia.org/wiki/Miosiren

[typhlonectes]

One Mountain, Two Tigers: A New Species of Gloydius (Serpentes: Viperidae) from the Upper Lancang Valley in Xizang, China, with Comments on the Diagnostic Characters and Evolution of the G. strauchi (Bedriaga, 1912) Species Complex

Jinlong REN, Junjie HUANG, Wei WU, Ke JIANG, Jiatang LI

Abstract

The Hengduan Mountains Region (HMR) in China, a globally significant biodiversity hotspot, has garnered attention for its potential to harbor cryptic species within the Asian pit viper genus Gloydius Hoge & Romano-Hoge, 1981. Based on comprehensive morphological comparisons and molecular phylogenetic analysis of the Gloydius strauchi complex, this study identified a previously unrecognized species of Asian pit viper. Discovered in the upper Lancang (Mekong) hot dry valley of Xizang, China, this species is geographically proximate to G. huangi but exhibits clear morphological distinctions from other members of the genus, representing the second Gloydius species identified along the upper Lancang River. We describe here this new species and highlight the significance of skull and hemipenis morphology, which were instrumental in its diagnosis and in resolving taxonomic boundaries and ambiguities within the G. strauchi complex. This study provides insights into the phylogenetic relationships and evolutionary history of this newly described species, enhancing our understanding of diversification patterns in this genus.

Read the paper here:

One Mountain, Two Tigers: A New Species of <italic>Gloydius</italic> (Serpentes: Viperidae) from the Upper Lancang Valley in Xizang, China, with Comments on the Diagnostic Characters and Evolution of the <italic>G</italic>. <italic>strauchi</italic> (Bedriaga, 1912) Species Complex

[arminreindl]

Tewkensuchus: King of Punta Peligro

Last month we got our fourth croc of the year and our second notosuchian: Tewkensuchus salamanquensis (Forehead crocodile from the Salamanca Formation), a large-bodied sebecoid from the earliest Paleocene of Argentina. And GODDAMN is it a cool one.

Below some of the fossil material of Tewkensuchus, it doesn't look like much but stay with me for this post.

Starting with the fossil material, Tewkensuchus is admittedly not the most complete sebecid, hell Dentaneosuchus from two years ago is significantly better preserved. Essentially, Tewkensuchus preserves a bit of the skull and a few vertebrae. But the material we do have is exceptional in other ways. Like some European sebecoids, it had a high and broad sagittal crest that extends over its forehead flanked by two broad depressions. Remember the similarity to European sebecoids, thats gonna come back later. Theres also some interesting stuff in how the bony eyebrows, the palpebrals, articulate with the rest of the skull.

What is REALLY weird however is the shape of the postorbitals. Quick anatomy lesson, in crocs the postorbitals form the front corners of the skull table thats located just behind the eyes. They tend to be flat, but in the case of Tewkensuchus they are inclined so that they rise upwards behind the eyes. Now we have plenty of examples of crocodylomorphs with raised squamosals, giving them a somewhat ear-like appearance, but raised postorbitals are a new one.

Below: An artistic interpretation of Tewkensuchus featuring its unique cranial morphology by Manusuchus (give them a follow) from different angles.

One last thing on its anatomy, it was BIG. And I mean big. The team that described Tewkensuchus estimate that its complete skull might have been just over half a meter long, so some 20 inches. This might correspond to a weight of perhaps 300 kg (660 lb), larger than even the largest Cretaceous Baurusuchids.

Now, I hope you remember the part where I said that theres similarities to European sebecoids. Well that sentence has two key points the paper deals with. First of all, the connection to European forms itself. Phylogenetic analysis seems to indicate that despite being found in Patagonia, all its closest relatives are from the Eocene of Europe. These are the recently named giant Dentaneosuchus from France, Bergisuchus from Germany and Iberosuchus (I'll let you figure that one out for yourselves). So after Tewkensuchus disappears South America is inhabited by only distant cousins while its closest relatives show up some 20 million years later on the other side of the Atlantic.

The other noteworthy part of the statement is the use of "Sebecoid" rather than sebecid. That's because of taxonomic back and forth. Essentially, a few previous studies have not included European sebecoids (Bergisuchus and Iberosuchus) within the family Sebecidae, instead featuring them as a separate branch that split off beforehand. In some studies that branch is known as Bergisuchidae, in others they are two branches, you get the idea. Now the description of Dentaneosuchus for instance did away with Bergisuchidae and simply include these European forms within Sebecidae itself. Still as the basalmost members, but given the honor of being at least included. Same goes for Ogresuchus. Well, in the description of Tewkensuchus, we go back to the separate model. So Bergisuchus, Iberosuchus, Dentaneosuchus and Tewkensuchus all form a single not officially named group simply referred to as the "Eurogondwanan clade". This group was placed as the sister family to Sebecidae and together with Ogresuchus the two form the newly named Sebecoidea.

Europe's sebecoids, Dentaneosuchus (art by Joschua Knüppe), Bergisuchus (by Scott Reid) and Iberosuchus (once again Manusuchus)

And this is where we need to address the fact that Tewkensuchus creates a bunch of new problems and makes old ones worse. For starters, it's size. By all accounts its way too big. Keep in mind, this animal appeared some 2 to 3 million years after the extinction of the dinosaurs, an extinction event that is generally thought to have killed everything on land heavier than 10 kilos. And then you get Tewkensuchus with an estimated weight of 300. Well, there's two possible explanations for that. Explanation 1 hinges on the known fact that these rules don't quite apply to semi-aquatic animals. Sure, anything large on land got whiped out, but eusuchian crocodiles managed to survive quite well despite their large size in part because they were partially aquatic. So perhaps Tewkensuchus and sebecoids as a whole underwent an aquatic phase? Well, this would work quite well with what is known as the Sebecia-hypothesis. Essentially, there is some debate on the relationship between sebecids and other notosuchians. Some studies draw a link between them and the similarily terrestrial baurusuchids, placing them in the group Sebecosuchia. Other studies meanwhile believe that sebecids are most closely related to peirosaurids, which in turn are close kin to itasuchids and mahajangasuchids, with both of the latter being more semi-aquatic than other notosuchians. The problem with this is twofold. On the one hand, to my knowledge there has never been any indication that sebecids underwent an aquatic phase and even Cretaceous sebecoids like Ogresuchus from before the impact were clearly terrestrial. The other issue, as nice as this would fit with the Sebecia-hypothesis, this particular study actually recovers the Sebecosuchia model. So there's that.

Personally I don't really buy into this explanation, which takes us to the second possibility. Sebecoids got really jacked really fast. I mean, that's it really. If sebecoids didn't undergo some weird little phase that somehow excempts them from the 10 kilo rule then the only logical answer is that they must have grown to a ridiculous degree the second the dust settled. Do we have evidence for that? Well....kinda but not really no. The closest we have is the fact that Dentaneosuchus from the Eocene clearly reached an enormous size on its own, but that was over 20 million years after the impact. We do at least know that sebecoids were small prior to the KPG thanks to Ogresuchus from Spain, which grew to only a meter in length. But a sample size of one isn't exactly exact proof that all sebecoids were small prior to the impact, especially with shifting phylogenies. The paper itself argues that its most parsimonious that whatever sebecoid crossed the boundry was already fairly large, but time will tell if this holds up. Whatever the case, with a skull half a meter in length it was certainly a formidable predator and a terrifying sight to any unfortunate mammal to cross its path.

Tewkensuchus attacking a startled Monotrematum, a South American monotreme, art by Joschua Knüppe

Finally the last thing to address, paleogeography. It sucks. Moving on. Jokes aside, sebecoid geography was already a pain in the ass. Assuming the sebecosuchian model, sebecoids likely split off from baurusuchids during the Santonian. Mind you this is purely based in the first appearance of baurusuchids, since sebecoids didn't appear for quite a while. Ignoring the problematic Doratodon, the first sebecoid to appear in the fossil record is Ogresuchus in the Maastrichtian of Spain. In the Paleocene we then obviously get Tewkensuchus representing the Eurogondwana clade in Argentina as well as sebecids proper, which seem to be constrained to South America. But then in the Eocene we suddenly have sebecoids in Europe and Africa (for simplicity I'm assuming that Eremosuchus was a sebecoid rather than a sebecid as is traditional). So, how does any of this work? We don't know. I've been breaking my head over how to best explain this without just repeating the paper itself, so let me just say this. Maybe sebecoids originated in South America with baurusuchids, they managed to enter Europe at the very least once giving rise to Ogresuchus, probably via Africa given that its very much undersampled. From there who fucking knows. Maybe Ogresuchus was just one random branch and the two main groups both actually originate in South America. Maybe the Eurogondwana group emmigrating to Europe as well while sebecids proper remained. Maybe the Eurogondwana group originated in Europe and Tewkensuchus simply returned to South America, or maybe they originated in Africa and had members travel west to South America and north to Europe. Or maybe....you get the idea, we don't know. We don't know if they rafted or took land bridges (tho the latter seems more likely), we don't know where certain groups first originated in actuality, we do not know a lot and Tewkensuchus being such a blatant link between Paleocene South America and Europe, which were well separated by that point, raises so many questions.

I imagine this is what this entire last section reads like....

I wish that last segment wasn't as chaotic as it is, but like I said, its a big old confusing mess and it gives me a headachse just thinking about it. So for the time being, its simplest to assume that they split from baurusuchids in South America and then some stuff happened we don't understand. Personally, I'm very much putting my trust in Africa here, I am 100% convinced that some very important stuff went down that we just haven't found yet. But thats just me.

[thestuffedalligator]

Debate about the evolutionary history of the common leprechaun (Sutor hibernicus) enters its second century, scholars split on the lines of leprechauns as dwarves (family Montihominidae) or leprechauns as pixies (family Puerihortidae). Genetic analysis reveals that leprechauns are descendants of the Irish hare (Lepus timidus). The chamber of magical phylogenetics explodes in rage.

[autistichalsin]

Mind Flayers and prions: a scientific analysis

Earlier today, I did some brain-related research for a fic of mine, and had a horrifying realization: what the hell happens if a Mind Flayer, which exclusively eat brains, catches a prion infection? A normal Mind Flayer is terrifying enough, now imagine one with kuru!

Then it was suggested to me that Mind Flayers would likely be immune somehow. And yeah, that seems like the second-most Occam's Razor-compliant theory (the first being that prions don't exist in Faerun, but come on, I'm a fucking biology nerd with a Masters in epidemiology and a love of parasitology, the odds of me making it that easy were fucking zero). But the question is: how would that work biologically?

So then I started with a deep-dive into prions in our world, and got my answer from a study on transgenic mice.

Before I get into that, though, I want to lay out the assumptions I'm making here:

Prions exist in Faerun, are capable of infecting humanoids, are found at the same locus (the Prnp gene that codes for PRion Protein [PRP] is located on the short arm of chromosome 20), and are transmitted the same way (in this case, the most relevant is consumption of infected brain tissue).

Considering that in Forgotten Realms canon, Mind Flayer tadpoles can't be inserted into dwarves, gnomes, etc (BG3 diverged from canon in this, and I can't blame them, it would be a sad and lonely game without little folks around), Mind Flayer DNA most closely resembles humans, but is obviously different from human DNA in more areas than elves or orcs (who we will assume are much more closely related to humans given that they can reproduce together) are to humans. That is to say, elves and orcs are closer to humans on the phylogenetic tree than mind flayers are, but mind flayers are still close to all of these, most especially humans.

The genetics of all organisms in Faerun are fundamentally the same as ours. The proteins and respective codons are the same, their form and function and significance are the same, they use the same five mammalian nucleotide bases... you get the picture. Minor genotypic differences are definitely there, but we're going to assume the foundations that inform our understanding of genetics as a whole are the same.

So, then. First, a very brief introduction to prions, because many people have never heard of them aside from possibly knowing about "mad cow disease" (feel free to skip this if you do already know):

The word prion is derived from the words protein and infection. It's exactly what it sounds like. It's a protein that is also an infectious agent, not a virus of bacteria. It exists as a wrongly-folded protein, and is very resistant to protease (enzymes that normally would break down a problematic protein). Over time, due to their resistance to proteolysis (the process that breaks down proteins)*, they eventually can force other proteins to misfold.

*Seriously, it can't be understated how terrifyingly resistant these things are. They can be inactivated with bleach, yes, but they resist autoclaves. You have to subject them to heats of 900 degrees Fahrenheit to denature them. For reference, the inside of a volcano is usually about 2,200 degrees.

The shape of proteins is extremely important in how they function, and proteins really want to be as parsimonious as possible; they want to use the lowest amount of energy possible to find a stable shape. The misfolded proteins require a lower energy expenditure than the normal form to maintain their shape, which is also more stable (hence its resistance to denaturing by heat), so normal proteins adopt it quite readily once exposed. From there, gradually (as little as months to as much as years) the proteins all convert to this unusual state. Unfortunately, while it's more stable for the individual proteins involved, it's a lot less stable for the brain itself, and the cells there begin to clump in amyloids, which cause brain damage and ultimately death. Prions are 100% fatal and care is limited to comfort measures. They also cause probably the worst symptoms of any disease I can think of. For example, the worst one of all, Fatal Familial Insomnia, literally causes sufferers to become unable to sleep. They start with extreme trouble sleeping, then over the course of a year find themselves gradually able to do it less, until one day they can't at all. Death follows in a few months, by which point it's downright merciful because they've been plagued with pain, paranoia, loss of memory, disorientation, headaches, weight loss, and more.

Prions are transmitted in a few ways: as noted, eating infected animal tissue is a big one, and was what led to the "mad cow disease" outbreak in the UK in the 1990s; cows were fed food containing the brain matter of other diseased cows, picked up the disease, and were then turned into food which infected quite a few people. Other ways are through contaminated medical equipment (as noted, you need to basically nuke medical equipment from orbit when it's used on someone with prions, and the long time from exposure to disease onset means a lot of patients are sick unknown to themselves or doctors), through genetics (IE Fatal Familial Insomnia), or sometimes even through spontaneous development if you're one of the unluckiest people on Earth.

So that's your primer on prions. Genetics, I'm going to assume some knowledge here, but I will give a brief explanation (brief because I don't want to seem like I'm just giving a thinly-veiled biology lecture).

The way genes code for proteins is by a series of codons, which are sequences of three nucleotide bases (A, C, G, and U/T depending on whether it's DNA or RNA) that are read and translated by the body. Most of the DNA in your body is non-coding and doesn't do anything, but the regions between a start and stop codon are what are used to make the proteins you need.

The gene that is implicated in prion diseases is known as Prnp, and produces the prion protein (which in its normal state is called PRPc and in its diseased state is known as PRPsc [sc standing for scrapie, which was the first prion disease to be discovered]). It is located on the short arm of chromosome 20. What it does normally is a bit of a mystery still, but the most widely believed hypotheses are cell adhesion or neuronal communication.

So, most mammals are really susceptible to them. Deer in the USA are currently suffering from a massive outbreak of one called Chronic Wasting Disease, humans have quite a few that affect us, and there are some notable ones in sheep, cows, etc. Even cats can get it. Rabbits are believed to be immune, but when scientists did an experiment with transgenic mice that forced them to express the lapine version of the Prnp gene, scientists could still force the protein to misfold by infecting the mice with prions, which suggests their immunity isn't absolute.

On the other hand, canines are also resistant, and scientists who tried to infect transgenic mice in the same manner after making them express the canine version of the gene had no luck (study can be found here). In wild type mice, the attack rate by the prions was 100%, but in the ones with the canine PRP, the attack rate was 0%.

We're getting a bit closer to our answer, then: clearly dogs have a gene that confers protection to their PRP, and since mind flayers most closely resemble a mammal (despite not reproducing the way humanoids do), the answer to mind flayer immunity would likely lie in the same gene.

As for the gene itself? Turns out, dogs have a codon at this locus that is found in very few other mammals. They contain codons that make, depending on the particular base pairs involved, either ASP (aspartic acid) or GLU (glutamic acid). This is not only rare (to the point of occurring in only a few other mammals), but provides a useful comparison: the PRP cats express is the most similar to a dog's. The feline Prnp gene doesn't include codons to make GLU or ASP. Cats are highly susceptible to prions.

So, while the why is still unknown and the correlation not proven yet as a causal pathway, it seems there is very likely a significant link between GLU/ASP production on that locus and the protection conferred to dogs against prions.

SO, finally, we can answer the question. Could mind flayers be safe while eating a diet of exclusively brains, even if they ate the brain of a creature infected with a prion? Yes, they could, assuming their Prnp gene has codons to produce ASP/GLU proteins as part of their PRP. And really, when you think about it, this would be yet another way illithids would claim to be superior organisms; while humanoids have to worry about an incurable neurodegenerative disease caused by something as trivial as an error in protein folding, illithids are conferred immunity by the ceremorphosis process. So it makes sense for the psychology of mind flayers that they're immune, too. And hell, they might even seek out humans infected with one, given they'd be weaker prey, the same way wolves just love to eat moose infected with a fatal brain parasite- and in turn, just like that protects the rest of the moose herd from being infected, illithids consuming sick humanoids would protect other mammals in the area too. It's certainly the kind of thing goodest squid Omeluum would do.

Thank you for coming to my TED Talk.

[max1461]

If you read about the anatomy of sponges they are so much simpler and... "single-celled adjacent" than comb jellies. It's like obvious they're older. I mean obviously simpler=/=older but it's the way that they're simpler which makes them seem older. Anyway. IIRC the main bit of research which suggests comb jellies are more basal is computational phylogenetics, which... look, biology isn't lucky enough to have regular sound change and a comparably robust comparative method like linguistics, and computational phylogenetics is much more underdeveloped in linguistics, etc. etc. etc. But my intuition is very much "if your statistical algorithm says one thing and comparative analysis overwhelmingly points in the other direction, trust the comparative analysis." But, look, I don't know. Maybe my intuitions aren't tuned to biology, or maybe there's other evidence that comb jellies are more basal, idk.

[kick-a-long]

An Israeli company may have brought back a thousand years extinct myrrh tree. They grew an ancient seed and they are still trying to figure out what tree it is.

Pretty neat. So that’s the date palm and a myrrh tree.

[mindblowingscience]

Ceratopsians are most famous for the triceratops, but the beaked family of herbivorous dinosaurs also included numerous other relatives throughout the Late Jurassic to Late Cretaceous Periods. Recently, however, a set of bone fragments revealed a totally new, much smaller primitive ceratopsian species—the most easternmost of its kind ever found in Asia. Given initial dating estimates, the dinosaur may also reinforce theories of how these unique animals migrated to modern-day North America roughly 110 million years ago. Sasayamagnomus saegusai is described in a September 2 study published by an international research team in the journal Papers in Palaeontology. Based on their analysis, they believe Sasayamagnomus helped form a distinct neoceratopsian clade—a phylogenetic group composed of a single ancestor and all its lineal descendants—along with North America’s Aquilops americanus and China’s Auroraceratops rugosus. With this new information, researchers argue for a revised evolutionary timeline that saw ceratopsian migration across continents occur during the late Aptian or early Albian age, somewhere between 113-110 million years ago.

Continue Reading.

[new-dinosaurs]

Rufiphonia Vázquez-López & Hernández-Baños, 2024 (new genus)

(A male individual of Rufiphonia rufiventris, photographed by Hector Bottai, under CC BY-SA 4.0)

Meaning of name: Not explained by authors, but presumably Rufiphonia = rufous [in Latin] Euphonia [genus of finches including the white-vented euphonia]

Species included: R. rufiventris (rufous-bellied euphonia, type species, previously in Euphonia), R. anneae (tawny-capped euphonia, previously in Euphonia), R. cayennensis (golden-sided euphonia, previously in Euphonia), R. fulvicrissa (fulvous-vented euphonia, previously in Euphonia), R. gouldi (olive-backed euphonia, previously in Euphonia), R. imitans (spot-crowned euphonia, previously in Euphonia), R. mesochrysa (bronze-green euphonia, previously in Euphonia), R. pectoralis (chestnut-bellied euphonia, previously in Euphonia), and R. xanthogaster (orange-bellied euphonia, previously in Euphonia)

Age: Holocene (Meghalayan), extant

Where found: Humid forests in Central and South America

Notes: Rufiphonia is a genus of euphonias, a group of finches from the tropical Americas in which the males tend to be brightly colored. Unlike most other finches, euphonias feed primarily on fruits instead of seeds, and accordingly they generally have less robust beaks than typical finches.

Currently, only two euphonia genera are recognized, Chlorophonia and Euphonia, each containing a large number of species. However, a new study on the evolutionary history of this group suggests splitting Chlorophonia into two distinct genera and Euphonia into three based on their phylogenetic relationships and anatomical differences. For species traditionally classified in Euphonia, the authors propose limiting Euphonia proper to a group of closely related euphonias in which males tend to have a dark blue throat and yellow belly, resurrecting the old name Phonasca for a second group in which males tend to have a yellow throat, and coining the new name Rufiphonia for a third in which both males and females can have rufous patches on the belly, head, or underside of the tail.

Reference: Vázquez-López, M., S.M. Ramírez-Barrera, A.K. Terrones-Ramírez, S.M. Robles-Bello, A. Nieto-Montes de Oca, K. Ruegg, and B.E. Hernández-Baños. 2024. Biogeographic factors contributing to the diversification of Euphoniinae (Aves, Passeriformes, Fringillidae): a phylogenetic and ancestral areas analysis. ZooKeys 1188: 169–195. doi: 10.3897/zookeys.1188.107047

[talon-dragonbeast]

hi! can you talk more about the significance of the biological concept of species? I'm a nonhuman who currently believes that species can't exactly be interpreted the way gender is, but I lack the vocabulary and knowledge in ecology to properly communicate that lol, so I thought I would ask you as an alterhuman in science! no worries if you don't feel like answering this ask :3

ooh i can definitely talk about that, yeah!! i was meaning to make a post like this since forever, so thanks for giving me the excuse!

so, i want to begin by emphasizing that species identity is a very real concept that should be always respected. of course, im an otherkin myself, so i dont think anyone ever doubted it in the first place, but i wanted to make myself clear anyways. species-diverse folks are the species they say they are, regardless of ones own beliefs. if a dog therian says theyre a dog physically, i believe them. if someone who looks like a human to me insists theyre not human at all, i believe them. if someone tells me, an atheist, that theyre a god or an angel, i believe them. and if someone says they can transform into a unicorn-dragon-zombie with robot wings through fucking magic, i believe them. so, now that that is clear, lets begin.

traditionally, species were classified based on their morphological characteristics, that is, their physical appearance. while this method was effective at first, it quickly became too unreliable (as evidenced by the many bird species that look almost the same, and dog breeds that, despite their physical differences, belong to the same species), so scientists began categorizing species based on their reproductive compatibility, specifically whether they could interbreed and whether their offspring were fertile. so, for example, iguanas and monitor lizards are incapable of interbreeding (different species), whereas donkeys and horses can produce mules, which are sterile (different species, same genus). finally, dogs and wolves can interbreed and they produce fertile offspring (same species, Canis lupus). nowadays, we classify species via phylogenetic analysis, which looks for similarities in DNA chains, though this method also presents its own problems as described by @nisaetus-nerd in this post.

now, why is species identity different from gender identity? well, for starters, species is more akin to biological sex than to gender. aside from the fact that the majority of the population takes species identity to be some kind of hilarious joke, species, just like sex, has some physical characteristics that (for now at least) cannot be changed. the category that we know as sex is actually a combination of chromosomes, reproductive organs (internal and external), external characteristics, hormones, (not relevant to humans but) pheromones, and reproductive cycles; similarily, species is a combination of many things, including DNA, physiology, morphology, diet, ecology, and behavior, among others.

its also important to point out that within the different sexes that exist in the human species there arent that many variations from one another; humans dont actually have a ton of sexual dimorphism (at least compared to freaks of nature (affectionate) like birds of paradise) and many of the differences between sexes that society highlights don't actually exist (think "female brain vs. male brain"). sex, at least in my opinion, isnt that important outside of reproductive health, so not many problems arise from simply throwing it out the window.

meanwhile, we do use species for a lot of things! as a vet in training, this is especially important when treating different animals; you wouldnt use the same drugs for a dog as you would for a horse, nor would you give the same food to a cow as you would to a pig. species are too different from each other, especially the further down the phylogenetic tree you go. you can actually use similar drugs for a dog and a human being, because we evolved together and have a similar physiology, but the same cant be said about chickens. most mammals heal their bones in a similar way (only difference i can think of, aside from the drugs, is the fact that you have to protect the bandages so they dont rip them off), but when it comes to, say, a bird of prey, thats an entirely different story. not to mention bees! they dont even have bones!!

(species have other uses outside of health of course, thats only what i specialize in. someone who studies ecology, or zoology, or genetic engineering, or any other field of biology would give you a different answer than mine. this is only my point of view, which i admit is kind of limited)

so! to wrap up this extremely long post, i want to stress once more that we need a term to express the experience of species identity, similar to how gender is discussed in transgender communities. species identity is not the same as biological species, and its crucial to be able to freely describe this experience with our own vocabulary. the way things are, biological species is too important of a concept to dismiss its meaning entirely, which is why we often face ridicule and skepticism when discussing it outside of alterhuman circles. the way we define "species" in our community (in which species = identity) is quite different from how most people usually understand the term (in which species = biology), and i think this misunderstanding is in part what leads to doubt when we talk about our experiences with others. so by changing the way we talk about species identity, we could get more people to understand what we really mean, instead on assuming based on the words we use.

[herpsandbirds]

Direct evidence of frugivory in the Mesozoic bird Longipteryx contradicts morphological proxies for diet

Jingmai O’Connor, Alexander Clark, Fabiany Herrera, Xiaoting Zheng, Han Hu, Zhonghe Zhou

Summary

Diet is one of the most important aspects of an animal’s ecology, as it reflects direct interactions with other organisms and shapes morphology, behavior, and other life history traits. Modern birds (Neornithes) have a highly efficient and phenotypically plastic digestive system, allowing them to utilize diverse trophic resources, and digestive function has been put forth as a factor in the selectivity of the end-Cretaceous mass extinction, in which only neornithine dinosaurs survived. Although diet is directly documented in several early-diverging avian lineages, only a single specimen preserves evidence of diet in , the dominant group of terrestrial Cretaceous birds. Morphology-based predictions suggest enantiornithines were faunivores, although the absence of evidence contrasts with the high preservation potential and relatively longer gut-retention times of these diets.  Longipteryx is an unusual Early Cretaceous enantiornithine with an elongate rostrum; distally restricted dentition; large, recurved, and crenulated teeth; and tooth enamel much thicker than other paravians. Statistical analysis of rostral length, body size, and tooth morphology predicts Longipteryx was primarily insectivorous.  Contrasting with these results, two new specimens of Longipteryx preserve gymnosperm seeds within the abdominal cavity interpreted as ingesta. Like Jeholornis, their unmacerated preservation and the absence of gastroliths indicate frugivory.  As in Neornithes, complex diets driven by the elevated energetic demands imposed by flight, secondary rostral functions, and phylogenetic influence impede the use of morphological proxies to predict diet in early-diverging avian lineages.

Read the paper here:

Direct evidence of frugivory in the Mesozoic bird Longipteryx contradicts morphological proxies for diet: Current Biology (cell.com)

[alphynix]

Allenypterus montanus was an unusual early coelacanth that lived during the late Carboniferous, around 324 million years ago, in a tropical bay covering what is now central Montana, USA.

Up to about 15cm long (~6"), its tapering tadpole-like body plan somewhat resembled that of modern knifefishes and featherbacks, with the top part of its tail fin highly elongated into a ribbon-like shape and the rest of its tail fins being vestigial. The distinctive humped shape of its back was also much more pronounced in larger, more mature individuals.

It was probably a fairly slow swimmer, and preserved gut contents suggest it mainly ate small soft-bodied prey.

Its closest known relative seems to have been the eel-like Holopterygius – but since around 60 million years and different continents separated them both, this suggests the existence of a whole ghost lineage of other tapering coelacanths yet to be discovered.

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References:

Friedman, Matt, and Michael I. Coates. "A newly recognized fossil coelacanth highlights the early morphological diversification of the clade." Proceedings of the Royal Society B: Biological Sciences 273.1583 (2006): 245-250. https://doi.org/10.1098%2Frspb.2005.3316

Lund, Richard, and Wendy Lund. "New genera and species of coelacanths from the Bear Gulch Limestone (Lower Carboniferous) of Montana (USA)." Geobios 17.2 (1984): 237-244. https://www.academia.edu/download/66985268/s0016-6995_2884_2980145-x20210504-8876-dzniic.pdf

Lund, Wendy L., Richard Lund, and G. Klein. "Coelacanth feeding mechanisms and ecology of the Bear Gulch coelacanths." Compte Rendus du Neuvième Congrès International sur la Stratigraphie et la Géologie du Carbonifère 5 (1985): 492-500. https://www.researchgate.net/publication/285577607_Coelacanth_Feeding_Mechanisms_and_Ecolqgy_of_the_Bear_Gulch_Coelacanths

Toriño, Pablo, Matías Soto, and Daniel Perea. "A comprehensive phylogenetic analysis of coelacanth fishes (Sarcopterygii, Actinistia) with comments on the composition of the Mawsoniidae and Latimeriidae: Evaluating old and new methodological challenges and constraints." Historical Biology 33.12 (2021): 3423-3443. https://doi.org/10.1080/08912963.2020.1867982