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Middle Amazon; Specimens 11.5 mm SL ground color creamy brown; small melanophores are scattered over the lateral body, with the exception of the abdomen region. There are more numerous melanophores on the dorsum of the head, the snout, and the anterior portion of lower jaw. Dense dark coloration lie ventral to the dorsal-fin rays, becoming less numerous posterior along the fin. The caudal and anal fin have a few melanophores along the fin ray giving it an appearance of it being slightly banded. The anal fin additionally has a superficial dark banding along the fin base.The pelvic fin is unpigmented. In specimens around 12-14 mm SL, the melanopores are more numerous, and larger, and are present over the body, except the abdominal region. The primary difference between these two specimens discussed and described is the dense melanophore concentration at the caudal-fin base, forming a dark caudal blotch. In addition, there is a thin band of melanophores ventrally encircling the orbit.The adipose fin is unpigmented. When specimens are about 22 mm SL, concentrations of melanophores are visible along the borders of the caudal fin and anal fin (in those specimens or populations where there such borders). As this geographic form develops to maturity, it has a distinct dusky hue, with the exception of the abdominal area, which remains lightly pigmented. In larger specimens that this, the anal fin forms a dark border. Larger specimens from the middle Amazon, (over 150 mm SL) are heavily pigmented, including the pectoral, anal, dorsal, and caudal fins. The body lacks any reticulate pattern. Adults in breeding condition are very dark, with virtually no pigmentation pattern.
Upper Amazon of Peru; 32-40 mm SL are generally similar to the specimens described above, but there are more melanophores over the entire body, including the small peppery ones, even ventrally to the level of the pectoral fins over the abdominal area. Fins are relatively more dusky. Some of the specimens have a reticulated pattern on the body side, a fairly dense black band of pigment on the anal-fin base, and the caudal spot is quite large, extending onto the caudal-fin base and the anterior of the caudal-fin lobes. There is a fairly dense scattering of melanophores on the dorsal fin, giving it a banded appearance.
Central Amazon area; 59-68 mm SL are again similar to the above described specimens, with a relatively broad band at the anal-fin base and a concentration of melanophores distally on the anal fin. The caudal spot is less developed, but the anterior parts of the caudal lobes remain darkly pigmented; there is a posterior dark caudal band. The pectoral fins has melanophores only on the anterior margin of the first ray. The adipose fin is black-margined. Adults (109-159 mm SL) have numerous tiny melanophores on the body, with concentrations under each scale, but without the reticulated pattern as shown by the Upper Amazon (Peru) specimens described above. The spotting on the sides is less distinct than on smaller specimens. The caudal spot is absent, but a black bar extending from the caudal-fin base onto the dorsal and ventral lobes. Most of the caudal fin is pigmented, including the posterior border. The smaller area proximal is relatively lighter. The anal fin has a dark band along its base, in the scaled area, and a dark distal border. In the largest specimens, body spotting is restricted to the area between the lateral line and the anal-fin base. The dorsal and lateral portions of the body from just behind the head to the caudal-fin base are silvery gray, with red or orange pigment suffused over the area, increasing in intensity in the belly region between the isthmus and anal fin. Head orange to red, more intense anteroventrally; most of the head is dorsally dark gray, suffused with orange to red, especially posterior and ventrally. Eye silvery, with reddish pigment. The lower jaw is dark gray and posterior is the same red or orange as in the abdomen. The pectoral and pelvic fins are red-orange; the dorsal is dark gray-black; the adipose fin is black and hyaline distally; the caudal fin is blackish gray, with a pale sub terminal or posterior border (there is variance from this locality and other locality where hyaline area lies midway between the dark fin base and the dark terminal band).
Upper Paraguay; there was few if any variation found in this population from the others in the basins. None of the characters used could consistently place specimens in relation to their geography. Southern populations clearly range within the variation of the Amazonian and coastal populations, although southern specimens available do not encompass the total size range of Amazonian specimens.
The extent and color of the belly pigment is variable ontogenetically, individually, geographically, and according to water conditions in which the fish lives. Post juveniles tend to be brighter and have more coverage of red than larger adults; in many large specimens from throughout the range of this species, the red or orange color is pale and limited in area to the ventral belly. In large adult specimens, the body of the fish maybe be almost entirely black, with bright burnished-gold "spangles" over much of the body. Specimens captured in clear, darker waters are often darkly pigmented with reduced red or orange, at all ages. Pygocentrus nattereri is the most widespread member of the genus and may not consist of a single evolutionary lineage. It is extremely variable in pigmentation and spotting. Pigmentation even within populations can range from yellow through orange to red, with coverage ranging from only a small area in the belly to most of the belly and head. Dark spots can be found on rather large specimens in some populations, but are lacking in others.