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This is a submission for the Anatomically Correct Series
Sentient Skeletons are a staple in works of fantasy and horror.
Sentient Skeletons are commonly depicted as:
Given these characteristics, what species could the Sentient Skeletons have evolved from, and what evolutionary pressures would lead to such a creature?
Cephalopod strangeness:
I don't think this is very probable, but strange things happen. The most likely scenario I can think of is that an octopus has evolved to moving on land, and they are using actual skeletons to frighten the apex predator (humans) away.
Heikegani crabs are believed to have a survival advantage because their shells bear a resemblance to a human face. Legend says they are the souls of dead samurai. A similar strategy could be used by an octopus seeking to move from sea to land. Imagine an octopus that has come to have the appearance of a human skull. This could even be a shell, as relatives of the octopus had shells (and octopi today have a vestigial shell). Knobby appendages on tentacles might be seen to resemble parts of arms, legs, or ribs.
Some octopi are known to use shells as protection from predators, shells they borrow or find in the environment (this can include human containers like cups). They can open containers to extract contained food items, so octopi are capable of tool use. So why not use a human skeleton as a tool?
An octopus that was already using it's skull-like appearance to frighten humans away and it's tentacles moving in a skeletal manner gets a hold of an actual skeleton (or assembled bits of wood and bone to resemble one). For the sake of practicality, let's sat this octopus can extrude some substance (modified ink, solidifying mucus, whatever) allowing it to make the joints of the skeleton hold together. Octopi CAN move on land, but very awkwardly. What do octopi lack (other than lungs)? A skeleton.
Such octopi would need a reason to want to go on land. Perhaps they steal food from frightened humans. their already skeletal-looking tentacles and movements in water have prepared them for using what amounts to a human-shaped set of stilts. With intelligence and practice, they might even get skilled at it. I doubt they would be very strong on land, but they might reasonably be able to wave a weapon around and walk upright. Humans seeing such a sight might develop a superstitious awe of the walking dead and placate the thing with offerings of food brought to the shore to keep the dead from leaving the sea, thus reinforcing this odd behavior.
Night would be the obvious time for such things to come out. These cephalopods would have limited time out of water, but they would likely not enjoy the burning sun. The dark would cover inconsistencies in their appearance and behavior.
I'm going to go ahead and say its not possible without being a 100% magical construct. Sufficiently advanced technology probably will be able to make skeleton size and shaped robots that meet your criteria, but I don't think biology can.
Take a look at the various groups that use exoskeletons: insects, arachnids, and crustaceans. They are mostly quite small and still require a large number of legs to support their weight. Some aquatic crabs can get decently large thanks to the help they get supporting themselves by being underwater, but on land, no way.
Our skeletons act as support structure for muscles and tissue to attach to. Muscles can only contract, so all of our mobility comes from clever uses of leverage as muscles pull on the outside of our bones.
Your skeletal entities would require some sort of muscle tissue that is MUCH more dense than our own just to fit the size constraints. It also needs to be capable of operating INSIDE a skeleton that was design to be pulled on from the outside.
If they are "living" they need to eat and breath. So they somehow need to fit those systems along with circulation inside the confines of a sub-optimally designed shell.
The shell needs to be MUCH stronger than human bone, seeing as how it not only has to support the creatures, but contain all of the muscles and organs, and also not crack like an egg at the first glancing blow.
With some magical assistance, a large terrestrial crab could be gifted with a super-shell and super-muscles and transfigured to look vaguely like a human skeleton. At that point why not just re-animate a human skeleton with magical forces?
Since this is for Anatomically Correct, I'm going to assume a technological basis rather than magical. Clarke's Third Law remains true, and so does its inverse, so implementing the concept is "left as an exercise for the reader"; pick whichever version works for you.
Starting from the extremities, a skeleton clearly has no musculature - and yet the bones move. The only logical conclusion would be a system of motors embedded in the joints. A skeleton body must therefore be entirely mechanical and driven electrically. Evolution doesn't even come into it; skeletons are designed and built.
This fits fairly well with skeletons' well-documented tendency to come apart when hit, and then connect themselves back together. Instead of damaging the motors, quick-release bindings (similar to those used for ski bindings) allow the joints to disconnect. And naturally it's easy to clip the joints back together, if you know how the quick-release binding works.
If this is driven by motors, we need power for the motors. The skeleton could have one big battery, but that would be an obvious target for enemies and a single point of failure for the body, as well as having the problem of how to get that power around. Conveniently though, bones have volume; and for bones which need to be stronger and would need more powerful motors for movement, the bones are bigger. So each bone has its own power supply, driving the motor(s) attached to that bone, and we don't need any cables.
Of course this means the "bones" cannot actually be made of bone. Most likely they'll be some kind of strong metal tube surrounding the battery. A light grey powder-coated finish (especially if not cleaned regularly) could very well look like bone to a casual observer. They don't have to have the exact same number of bones as a human - perhaps the spinal column might be a single continuous strut, for example. No-one's going to look too closely when a dozen of these things are trying to rip your head off, after all.
If we want to hypothesise a reason why they might stay in the dark, perhaps the coating has a good lifespan in the dark (keeping the skeletons intact for centuries or millenia) but reacts badly to light. We have plenty of examples of synthetic plastics which last a very long time in the dark but break down under UV.
So how do we make each motor move? Simple: the skeleton runs a wireless network connecting all its parts together on the IoT principle. This means we don't need wires between the bones, which clearly is a good thing.
This also explains how a disconnected limb can "fight" on its own, or "crawl" back to the main body. So long as it is within range of the wireless network, it remains under control of the skeleton, and being self-powered it can function relatively independently if it has to.
The "eyes" of course are cameras which can see in IR and visible light. They include LEDs to provide illumination in complete darkness, the same as a security camera or many webcams. This explains why they often are shown with glowing eyes as the optical system switches between IR and visible illumination depending on what gives best resolution.
We have to figure out how this is being controlled. The control system naturally lives in the skull, because it's the only part of the body with significant internal volume. It also gives us the trope of needing a headshot to kill them.
The control system needs to be some kind of electronics. With electronics, the skeleton can power down for long periods until something wakes it up. (I considered the "disembodied head" concept, but there's too much handwavey pseudo-science in that.)
If we want our skeletons to be human-level intelligence, perhaps we have a consciousness upload system, which of course requires some very advanced technology. Most fantasy shows skeletons as relatively unintelligent though, able to respond to basic stimuli but not capable of complex thought and reasoning. So it seems much more likely that a Boston Dynamics type of AI control would be running this. Since BigDog and its like are basically there already, this would be perfectly possible with current technology.
With the skeleton then being a fully mass-manufactured robot, this would also explain why "necromancers" keep skeletons in storage by the thousand and simply swamp attackers with wave attacks. They cost resources to make, sure, but they can be stored powered-down indefinitely so you can build up your stock over time, and you don't need to worry about what happens to them in combat. And your "casualties" can be repaired relatively easily, because every component part of the skeleton can simply be replaced and the skeleton sent back out into battle again.
For anyone paranoid enough, the biggest risk is always other people. If you have money and/or power, paranoia has to be a way of life to some extent, because kidnapping is a risk - and the more money and/or power you have, the bigger the risk. And with political power too, assassination is also a risk. Even bodyguards don't help, because as Indira Gandhi found out, your own bodyguards may actually be the risk. No, the only way to be truly safe is to have your bodyguards being utterly incorruptible - and the only way to achieve that is for them to not be human in the first place.
This also fits with skeletons generally being animated and commanded by a solitary "necromancer" who avoids contact with other people. You need to be a sufficiently talented engineer to design and build this, sufficiently rich to afford parts, and sufficiently socially isolated that no-one notices your experiments until you already have your skeleton army built. Not necessarily a mad scientist - more just a rich but reclusive young geek who's sold their dotcom for a few tens of millions and headed off to the hills, away from interactions with people who scare them.
So, you build your skeletons. As a walking bag of bones, they're about as scary as it gets. That gets them an edge in a fight - and of course unless you're lucky (or skilled) enough to take out the head, they just get up and carry on when you chop bits off them. That's enough to deter pretty much anyone.
A long-term "sleep mode" also make them the perfect guard. They could even be left on guard in plain sight, with people thinking they're just a macabre decoration - until they attack. And if they're not needed for a longer period, a disassembled box of "bones" would take up remarkably little space.
But suppose the "necromancer" didn't want to be quite so overt about the nature of his bodyguards. The Terminator approach of putting skin over them is going to be fairly convincing, so long as no-one looks too closely. Kyle Reese even says that early models had rubber skin. If all the castle guards are on the other side of a portcullis (or security door if we're in more modern times), people likely would never notice. Most aspects of security theatre (uniforms, masks and so on) are even designed to dehumanise guards to make them appear more intimidating, going back to antiquity with scary helmet designs. Actual robots would simply appear to be normal people with good training.
They are a divergent evolutionary branch of homo sapiens, to be more precise of the homo sapiens subspecies toppus modellus.
At the times around the transition between 20th and 21st century, a particular variant of humans were highly priced in the current society. These humans were called model, and their salient physical feature was being really skinny.
While in certain environments of the human society there started to be an opposition to excessive slender bodies, in others being skinny remained highly appreciated.
Eventually some of these skinny people started living a separate life in a separate environment and, thanks to their lower food demand, somehow managed to thrive in the apocalypse which stormed away most of the other homo sapiens in the middle of the 22nd century.
Interbreeding and natural selection led to the emerging of individuals with extremely reduced muscular mass, to the point it required extremely close inspection to be told apart from what it looked like a skeleton. Also the abdominal region was highly reduced in volume, essentially paving the inner of the hip bones.
Nocturnal habits emerged as a consequence, to not waste resources in producing skin pigments.
Your sentient skeletons are actually a colony or swarm of stick and leaf insects working in unison. Many insects have a swarm, eu-social decision making ability that can border on sentience at times.
Rather than explaining why leaf and stick insects are working in unity, you could have the stick and leaf characterisitcs be based on male/female sexual dimorphism.
Each skeletal bone could be a single or multiple stick insects that give the impression on bones.
The long skinny bones would be either single or multiple stick insects. The larger "flatter" bones such as pelvis and skull would be multiple overlapping leaf insects.
This option also gives an simple explanation for dismembered limbs that continue moving on their own, often trailing behind the main body trying to rejoin the swarm.
Also explains why they are so hard to kill as in order to destroy the creature, you have to destroy every bone (or at least a large proportion) rather than damage a single organ.
Self explanatory. They do have insect organs but are hidden internally by their deceptive outlook.
With multiple limbs to grib objects, and ability to manipulate the angles objects are being held at as well as the weight distribution of the body, human like strength is achievable. (Think catapult/trebault and levers/pulleys counterweight logic).
Does being a stick (a rudimentary tool) count as tool use? No seriously, with swarm decision making logic similar to bees it would be fairly reasonable to explain away the simple manipulation of the component parts (bones) movements to control tools.
Lots of insects are nocturnal. Very easy to explain.
The stickleaf insect swarm evolving into a skeletal shape could be explained by mimicry.
Originally they feed off the decaying corpses laying around, over time they mimic the skeletal patterns they are surrounded with. Originally they would be simiple skeletal animal designs walking around but as their sentience evolved they would have mimicked more complex patterns they come across. Eventually settling on using the human shape as it's more adaptable for manipulating the random tools they found lying around (eg battlefields).
The clustering of male and females in certain region of the design would have evolved as the males stick design was more rigid and better suited for support structures while the leafy female insects clustered around to form broadwr flatter bones. With less body energy being assigned to keeping themselves rigid, the females were free to expend their body energies on more energy expensive features such as neural clusters. The female insects literally run this swarm!
Translucent fungus
This is a slight cheat on your condition that there be no visible muscles or ligaments, but imagine something similar to a slime mould, that has colonised the skeleton of a deceased human. I specify translucent because in low light, it would look mostly like just a self-moving skeleton. In real life, slime moulds are in a half-way state between being monocellular and multicellular organisms, but nonetheless are able to exhibit some surprisingly complex behaviour, such as "sniffing" out sources of food and directing other members of the colony to shift themselves to move in that direction.
So what I'd propose would be something similar to a slime mould that has wrapped itself around the bones of a skeleton, and then acts as its own musculature by forming strands of cells that can contract and release to push and pull on the bones. As the organism's lifecycle relies on colonising human skeletons, it will make sense that these colonies would want to seek new skeletons to infect, so these skeletons will be driven by simple chemical impulses to seek out living humans to kill and infect the corpse with their spores.
"Sentient skeletons" are clearly a variety of undead. They may even be zombies whose corpses have deteriorated to the point that no soft tissue remains.
Mind you, we are talking about a supernatural undead. These aren't your "freak virus causes zombie-like behavior" zombies of 28 Days Later, nor even the "we want it to be a microbe but show clearly supernatural effects" zombies of The Walking Dead.
These are your straight-up, supernaturally animated and probably by an evil force, zombies. With the flesh so decomposed that it fell off their bleached, white bones.
This means that no force of evolution is implicated in their existence. And given their anatomy, their origin is clearly human.
When anatomical skeletons are used (perhaps in a medical school), that skeleton has to be "articulated". The bones in your fingers (and elsewhere) aren't directly attached to each other. They don't have little ball-and-socket joints. If the flesh were gone, they would be unattached to each other and free-floating.
We can assume that some sort of limited telekinetic-like force animates these skeletons, but that the spirit doing so can only move those bones (rather than just force-choking enemies from across the room). Not only that, but that the spirit is mostly limited to moving the bones in ways that imitate how they'd move while still alive.
This goes a long way to explaining zombies too, since we no longer have to worry about how muscles far into decomp could contract/expand on command, and to do so with no blood circulating nutrients and oxygen. Zombies that have suffered wounds that would incapacitate a living person through absolute mechanical defect can still wander around, at least to the extent that their remaining corpse might allow.
