Colors ultimately, are pretty simple. The light color is the belly, darker colors create the back so your flies are countershaded just like the fishes they are imitating. The rest is really up to what you are imitating and your imagination. After all, flies like the Mickey Finn and many other patterns look nothing like anything you'll see in nature. Or take Lefty's advice - if it ain't chartreuse, it ain't no use! Which is why I bought the Bob Clouser custom tied fly in chartreuse, not that it will ever see the water, of course.
Because I am an unapologetic geek, I feel the need to explore the Bob Clouser fly. It looks more dense in the photo than it really is. In hand, the fly fly is noticeably front-heavy. The eye, on this shank is about 40% back from the eye. It balances a bit less far forward as my typical ties. The upper body is just the slightest bit shorter than the belly. And the belly is tied down the entire length of the shank and epoxied as are the eyes. The flash is rainbow (or something similar) Krystal flash. The belly and back are much more flat - compressed vertically - than I've tied them.
Shapes are a little bit more limited. Clousers best represent relatively elongate fishes (minnows, immature bass, trout, darters, etc.) and probably are not the best bet for imitating fishes like shad or Bluegill which are more laterally compressed. You can look back to part 1 of Project Clouser (link) and see how choice of materials can affect the shape of the fly. More specifically, on bucktail Clousers, choosing hair near the base of the bucktail will give it "taller" profile as well certain synthetics (typically those with a lot of "krinkle" to them). However, round or slightly flattened fishes are better represented by Clousers than are more flattened fishes.
Other than the body color, the eye color seems to be the next most malleable aspect of the fly. I honestly don't get overly concerned with eye color but I tend to go for something that will catch a fish's attention. If I could only choose one color, it would be bright orange - not that any fishes really have orange eyes. A second choice would be yellow/chartreuse. I don't really think it matters except that visibility is a good thing.
The Emerald Shiner (Notropis atherinoides) Example
Emerald Shiners are a very common minnow species in lakes and larger rivers across much of North America (details and range map). They are a fairly nondescript minnow with a whitish belly, an iridescent olive / blue / purple back, a rather pronounced eye, and a translucent body. The body shape is elongate and slightly laterally flattened. These are all things that are pretty easily captured in a Clouser Deep Minnow.
Source: iNaturalist (https://www.inaturalist.org/guide_taxa/719742)
Below are a couple of imitations of an Emerald Shiner that are tied sparsely to try to match the natural translucence of the minnows. Both of these are tied with the white bucktail belly tied down behind the eye and flash added behind those thread wraps and olive and blue fibers for the back.
The distinct bands (top fly) give the fly a more solid profile and the yellow eye is a little less obvious than the orange eyed fly below. I roughly counted the number of fibers in each fly so they're about the same number. However, the mixing gives the fly a much different, more transparent / translucent appearance. Does it really matter to the fish? Who knows but it might matter to me as I choose which one to tie on my tippet. Let's face it, flies are as much for us as they are the fish.
There are tons of options for Clouser coloration. Find the common minnows (shiners, chubs, minnows), sucker, darter, and other forage fish species in your area. Bass and trout are also quite cannibalistic so "baby bass" and trout patterns often work quite well.
Affecting the Shape of the Fly
There are a few ways that the fly tyer can alter the shape of the fly - material choice for the body, how much material is tied down, thread control when tying it down, etc. Probably easiest is the choice of materials. As mentioned in other Project Clouser posts, when using bucktail, what part of the bucktail you use will have a pretty significant effect on what the fly will look like. Want more spread and a taller or wider body? Take hair near the base of the tail. As you move towards the tip, you will produce a slimmer fly with the same amount of fibers. Similarly, the choice of synthetics will influence the shape of the fly.
While it is certainly not Fly Tying 101, experienced tyers can adjust thread tension and how fibers are controlled while they are tied in to affect the shape of the fly. The Clouser below uses brown deer tail fibers from closer to the base of the tail and it was pushed around the Ripple Ice Fiber to produce a fly that is more round in shape. To produce a "taller" fly - one that is laterally flattened - using coarse (kinky) bucktail fibers from near the base of the tail and holding them so they can only flare vertically and not horizontally.
Below is a good example of a sparsely tied Clouser with a good bit of body to it. What I like about this style is that on the pause, the fibers will relax and move back towards the shape in the photo and on each strip, they will compress.
Below is a Clouser with an olive-brown marabou back tied over bucktail. While it looks quite bulky when dry, it will take on a much different shape when wet. What I like about marabou is it has a lot of inherent movement. Each strip and pause will cause it to move. Being so soft, it can get wrapped around the hook. The bucktail belly is an attempt to prevent that from happening.
Lastly, the choice of synthetics used to tie the fly will affect the shape of the fly. Craft fur (upper left) has almost no flare but the soft fibers produce a significant amount of movement. Others like Congo Hair, a Flytyer's Dungeon product (lower left), has a lot more body to it due to the "krinkle" in the fibers. There really is no substitution for trial and error to see what different materials will look and behave like when used for a Clouser (or any other pattern). In general, synthetics with a lot of "crinkle" to them will produce more body and will be more transparent / translucent.
Matching the "Hatch"
Matching the hatch certainly means color and trying to mimic the naturals but probably more importantly than matching colors is matching the size (length) of the most abundant prey. For most fishes being imitated, smaller fishes are abundant in the spring and early summer and they grow as the summer turns to fall. Don't be caught without some smaller patterns, particularly in June and earlier. I remember an early June day on the Lower Wisconsin for smallies where I had nothing but three-plus inch imitations but all the minnows were two inches or less in length. Not accustomed to seeing many large minnows, my flies went largely uneaten until a friend shared a smaller fly more suited to the conditions. Size matters - and almost always it matters more than color.
To match the hatch, there are a number of resources to figure out what species of forage fishes are common where you are fishing. Unfortunately for Wisconsinites, the Wisconsin Department of Natural Resources fisheries sampling map is currently offline (linked in case it returns online) but as the page suggests, contact your local fisheries biologist for information. In cold streams (trout streams), sculpin and darters are common in addition to trout. As streams warm up a bit, dace, shiners, chubs, darters, and suckers become more common. Moving to larger rivers, small suckers and shiners - like the Emerald Shiner are most common. To see what these fishes look like, visit Wisconsin Fish ID from Sea Grant.
In summary, play around and practice tying slightly different shaped Clousers. The pattern doesn't allow a ton flexibility in shape but there are some things you can do to produce flies that are rounder or more laterally flattened. Longer or more compact. Color and flash are a lot easier to modify and the general pattern provides a great template for "messing around", otherwise known as experimentation.
Project Clouser Blog Entries
Introduction to Project Clouser (last week)