The first time I did squats as an exercise, I was 15, doing bodyweight squats in a martial arts class. I can't recall any specific instructions on how to squat, but the instructor squatted to a legal depth, so I did the same. When I was about 16 or 17, after a long time of nothing but leg presses for my lower body (which annoyed me; I actually wanted to have strong legs but no one wanted to teach me how to safely put a bar on my back in the power rack), bodyweight squats were reintroduced into my programming, but I still wasn't taught how to perform any kind of loaded squat. I can't remember an instruction on depth, but I do remember the instructor saying something about sitting back and keeping my weight on my heels. I don't know if his made my bodyweight squats any better or worse than they had previously been, but they were definitely different.
It wasn't until I was in Cert III in Fitness when I was 19 that I was taught barbell squats. I was taught them the same way every gym instructor knows is the correct way to do them: knees bend to 90 degrees and don't go past your toes -- however 90 degrees was intended just as a starter tip, on the premise that the average PT client is horrendously deconditioned and will do bad things if they go much lower, not with the assumption that squatting lower is bad if you have the coordination to do so. When I was studying my Diploma of Fitness the next year, I was taught that once you go below parallel, the hamstrings deactivate, and it became day-in-day-out rhetoric. For all of 2009, I knew that hitting parallel or going lower was always bad for you. Of course, then I finished my Diploma, and started researching from sources other than my lecturers. I discovered a thoroughly contradictory mantra to what I'd been taught before, that the deeper you squat, the more involved your hamstrings become. Which is right? Which is wrong? Well, actually, there's some truth to both of these claims.
I felt this space needed a picture.
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The truth is, hamstring involvement in any squat will be determined largely by hip angle relative to the knee angle. That's so important when analysing these claims from either side of the argument that it warrants repeating. Hamstring involvement in any squat will be determined largely by hip angle relative to the knee angle. If the range of motion at the hip increases, the hamstring involvement will increase (which is where those who say that increasing depth causes increased hamstring involvement get their argument from), however, if the range of motion at the knee increases, the hamstring involvement will decrease. Remember the basic actions of the hamstrings: hip extension and knee flexion. The basic movements of the squat are hip extension and knee flexion, so the movement of the hips load the hamstrings, while the movement of the knees deload the hamstrings. Whichever of those two joints has the greatest range of motion basically wins. Therefore, if the range of motion at the hips is 135 degrees, and the range of motion at the knees is only 100 degrees (angles that might occur in a powerlifting squat), there's potentially going to be a lot of hamstring involvement. Reverse those numbers so that the knees have significantly more movement than the hips, and the hamstrings will be doing very little, as we know to be true in front squats.
How does this apply, then, to partial squats? Well, if your limb lengths are anything like my own, then following the old advice of squatting to 90 degrees at the knees and keeping your knees behind your toes will (assuming you keep your back rigidly in neutral position and don't let your bum tuck under) result in the hips moving about 90-110 degrees, which of course means a greater range of motion at the hips than the knees, which enables a lot of hamstring involvement. If this statement (that squatting above parallel can in fact use the hamstrings a lot) offends you, go do a deadlift and figure this stuff out on your own.
The people who think of squatting to 90 degrees as standard tend also to think of keeping the knees over or behind the toes (never letting them pass the toes) as standard, also. These are the same people who say that squatting below parallel causes your hamstrings to deactivate. It warrants mentioning, at this point, that the further back you keep your knees, the further back your hips will be, since these rather rigid objects called femurs live between those two points. And the further back your hips go as you descend, the greater the range of motion will be at the hips. So then, what's going on with this claim (from the framework of keeping the knees back) that hitting parallel or lower deactivates the hamstrings? Surely these people would think otherwise, right?
Well, using their framework, they actually have a point. There are some people who can hit parallel with their knees behind their toes, and they are very glute/ham-dominant squatters. However, most people will do something wrong if they try this. Any of the following are reasonable to expect, and the consequences of any such blunders range from looking a bit silly and reduced productivity through to some pretty serious damage:
1. The lifter reaches the limit of their hamstring flexibility, and so they tuck their bum under to hit depth. Butt-tucking is really an act of unloading the glutes or hamstrings when they don't want to stretch any further, which takes tension out of the hip end of the hamstrings.
2. The lifter reaches the limit of their hamstring flexibility, and dips their knees forwards to hit depth. They couldn't keep their knees behind their toes, so at the last minute they let their knees pop forward, increasing knee flexion and again taking tension out of the hamstrings. It should be noted that most lifters who aren't hung up on keeping their knees over/behind their toes will let their knees drift forward earlier in the descent, so that the knees are as far forward as their needed for the required depth, and hamstring recruitment will then peak as the hips become parallel with the knees.
3. The lifter has the flexibility to hit parallel with the knees back, then keeps descending further, causing the hips to swing forwards as they come down. This isn't the same as the bum tucking under, as the spine remains neutral and the hips don't attempt to unload the built tension in them. If you ever watch an Olympic lifter squat, you'll see that their squats are generally ATG, but they're also still roughly parallel. Meanwhile, if you look at most powerlifters, the bottom of their squat his their hips still fairly high up off the ground. This is because the Olympic lifters typically let their knees drift further forwards, which also brings the knees closer to the ground, so for them to go ATG doesn't require them to go super-far below parallel (usually). Meanwhile, the powerlifter's shins will often be more upright, keeping the knees from drifting as far forwards, so that the hips will be further back to get the hamstrings firing hard for the lift. Once you hit parallel, because the femurs have a fixed length, the only way to stop the hips from swinging forwards as you descent any further is to pull the knees even further back, which is obviously not going to happen (and wouldn't be beneficial for keeping the hamstrings tight, anyway, since it would mean more knee flexion). Swinging the hips forwards does little (if anything) to increase the angle at the hips, but it does increase the angle at the knees. Such an action will take tension out of the hamstrings, rather than loading them any further.
Of course, if we remove the presupposition that the knees are supposed to stay directly over or behind the toes, and allow for knees to move forwards as far as is needed, then these issues are less likely to occur.
And that's all I feel like saying on hamstring involvement in squat right now. I'd like to note that while I've attempted to show that hamstring involvement can be quite high or quite low regardless of squat depth, and thus there's a bit of truth on both sides of the fence, this is in no way an attempt to say that squat depth is irrelevant when it comes to knee safety. There are a lot of things that could cause you to hurt your knees, of which faulty or subpar activation of the hamstrings is just one.
A video of lifter Tom Martin doing partial squats in a manner that probably gave his hamstrings
plenty of work.