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The numerous damselfishes of this genus are known for marked coloration and pattern changes as they grow, mostly converging on a uniform dusky appearance as adults. Pre-transitional larval Stegastes are mostly colorless with few distinguishing markings and overlap extensively in meristics and thus DNA sequencing is necessary to identify many larvae to species. Damselfish larvae rapidly acquire juvenile markings during the night of settlement and transitional larvae are common in collections over the reef, even before they have the chance to transform in a trap.

New recruits of some Stegastes species can share the markings that are used as species-specific diagnostic characters in the later juvenile stages. These shared markings include the pattern of spots and stripes on the head, the size, shape, and position of the dorsal-fin ocellus, the spot at the top of the pectoral-fin base, and the upper caudal-peduncle saddle-spot. These characters may not be consistent for identifying juveniles below 20 mm SL and many species identifications of photographs of small juveniles on the web and in reef fish guides are mistaken. Furthermore, the published descriptions of juveniles of this genus are almost always incongruent and depend on highly variable characters, such as shades of yellow or the degree of striping. The most egregious example of this is the commonplace assignment of any juvenile with blue head stripes to S. diencaeus.

Transient ontogenetic homologies in pomacentrid early life history: This interesting phenomenon of short-lived, presumably vestigial, markings that appear on early juveniles is somewhat analogous to the homologies in ontogeny shown in mammalian embryology. In this case, however, ontogeny may recapitulate phylogeny (in a way) as ancestral markings may persist in the earliest juveniles of an entire clade. The similarity may extend to the mechanism for the persistence: just as obsolete embryological structures persist because of reduced selection pressure within the womb (for example the hindlimbs in dolphin embryos), these early markings may persist because of reduced selection pressure for species recognition among the smallest juvenile stages on the reef. Alternatively, a more intriguing explanation may be that this phenomenon is an adaptation to disguise species identity at the time of extreme vulnerability to competitive interactions from adults.

Species Identification: Among the larval Stegastes, S. partitus diverges first during the transition phase by not developing the dorsal-fin ocellus shared by all of the other reef species. The dorsal-fin ocellus is the first transitional marking appearing on larvae. Immediately afterwards, the outlines of iridescent spots and stripes appear on the head and upper body and the spotted species, S. adustus and S. planifrons, can be distinguished from the striped species, S. diencaeus, S. leucostictus, and S. variabilis.

New recruits of S. partitus share the blue spots and stripes on the head characteristic of other Stegastes, although these are usually not conspicuous and disappear rapidly. Once the dorsal-fin ocellus develops, S. adustus and S. planifrons can be distinguished by having only spots, not stripes, on the top of the head (as well as other distinctive color patterns). The three remaining reef species, all with a dorsal-fin ocellus and stripes on the head, share most basic markings as new recruits (S. diencaeus, S. leucostictus, and S. variabilis). Nevertheless, with the characters described below, juveniles of these species should be categorized correctly. It should be noted, however, that intermediate individuals do occur. This is probably variability within species, although the possibility of occasional hybridization should not be excluded. DNA-sequencing analyses, underway at present on this group, will confirm the identification of larvae and new recruits of these species and explore the hybridization question further.

The most troublesome feature of juvenile markings in these damselfishes is the rapid change in the size, shape, and position of the spots, stripes, and the dorsal-fin ocellus. Overlying these ontogenetic changes is a high degree of variability within species. My DNA sequencing of these damselfishes reveals that many features are inconsistent for separating species at these early stages, especially the size and position of the dorsal-fin ocellus and the intensity of spots on the head and dorsal fin.

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