Breeding is seasonal and appears to be stimulated by the peak of long heavy rainfall and resultant flooding of shallow marshes, usually near Lake Victoria. This flooding is linked to an increase in prey fish availability; and reproduction is therefore synchronised with this peak in food availability. In such observations near Kisumu, M.P. Kahl's explanation for this trend was that in the dry season, most prey fish are forced to leave the dried-up, deoxygenated marshes that cannot support them and retreat to the deep waters of Lake Victoria where the storks cannot reach them. However, fish move back up the streams on the onset of rain and spread out over the marshes to breed, where they become accessible to the storks. By nesting at this time and providing that the rains do not end pre-maturely, the storks are guaranteed a plentiful food supply for their young.
The yellow-billed stork may also begin nesting and breeding at the end of long rains. This occurs especially on flat extensive marshlands as water levels gradually decrease and concentrate fish sufficiently for the storks to feed on. However, unseasonal rainfall has also been reported to induce off-season breeding in northern Botswana and western and eastern Kenya. Rainfall may cause local flooding and hence ideal feeding conditions. This stork appears to breed simply when rainfall and local flooding are optimal and hence seems to be flexible in its temporal breeding pattern, which varies with rainfall pattern throughout the African continent.
As with all stork species, male yellow-billed storks select and occupy potential nest sites in trees, whereupon females attempt to approach the males. The yellow-billed stork has an extensive repertoire of courtship behaviours near and at the nest that may lead to pair formation and copulation. Generally, these courtship behaviours are also assumed to be common to all Mycteria species and show remarkable homology within the genus Mycteria. After the male has initially established at the nesting-site and the female begins to approach, he displays behaviours that advertise himself to her. One of these is the Display Preening, whereby the male pretends to strip down each of his extended wings with the bill several times each side and the bill does not effectively close around the feathers. Another observed display among males is the Swaying-Twig Grasping. Here, the male stands on the potential nesting-site and bends over to gently grasp and release underlying twigs at regular intervals. This is sometimes accompanied by side-to-side oscillations of the neck and head and he continues to pick at twigs in between such movements.
Reciprocally, approaching females display their own distinct behaviours. One such behaviour is the Balancing Posture, whereby she walks with a horizontal body axis and extended wings toward the male occupying the nesting-site. Later, when the female continues to approach or already stands near an established male, she may also engage in Gaping. Here, the bill is gaped open slightly with the neck inclined upward at about 45° and often occurs in conjunction with the Balancing Posture. This behaviour ordinarily continues if the male accepts the female and has allowed her to enter the nest, but the female usually closes her wings by this time. The male may also continue his Display Preening when standing next to the female in the nest.
During copulation, the male steps onto the female's back from the side, hooks his feet over her shoulders, holds out his wings for balance and finally bends his legs to lower himself for cloacal contact, as happens in most birds. In turn, the female holds out her wings almost horizontally. The process is accompanied by bill clattering from the male as he regularly opens and closes his mandibles and vigorously shakes his head to beat his bill against the female's. In turn, the female keeps her bill horizontal with the male's, or inclined downward at approximately 45 degrees. Average copulation time in this species has been calculated as 15.7 seconds.
The female typically lays 2-4 eggs on alternate days and average clutch size has been recorded as 2.5. The male and female share duties to incubate the eggs, which takes up to 30 days. As in many other stork species, hatching is asynchronous (usually at 1- to 2-day intervals), so that the young in the brood differ considerably in body size at any one time. During food shortage, the smaller young are at risk of being outcompeted for food by their larger nest-mates.
Both parents share duties of guarding and feeding the young until the latter are about 21 days old. Thereafter, both parents forage to attend to the young's intense food demands. Alongside parental feeding by regurgitation of fish, parents have also been observed to regurgitate water into the open bills of their nestlings, especially on hot days. This may aid the typical thermoregulatory strategy of the young (common to all stork species) to excrete dilute urine down their legs in response to hot weather. Water regurgitated over the young serves as a water supplement in addition to fluid in their food, so that they have sufficient water to continue urinating down their legs to avoid hyperventilation. Additionally, parents sometimes help keep the young cool by shading them with their open wings.
The nestlings usually fledge after 50–55 days of hatching and fly away from the nest. However, after leaving the nest for the first time, the offspring often return there to be fed by their parents and roost with them for another 1–3 weeks.It is also thought that individuals are not fully adult until 3 years old and despite lack of data, new adults are thought to not breed until much later than this.
Fledglings have also been observed to not differ considerably in their foraging and feeding strategies from adults. In one investigation, four adult, hand-reared yellow-billed storks kept in captivity showed typical grope-feeding and foot stirring shortly after they were introduced to bodies of water. Hence, this suggests that such feeding techniques in this species are innate.
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