Broad groups of chick plumage
From the outgroup it was possible to select three broad groups of chick plumage colours and patterns by which to categorise the francolin and spurfowl chicks.
Plain: The darkish chicks of megapodes (Megapodiidae) are plain dorsally without stripes. The chick plumage of guineafowl species that live in the open understory of forests, such as Guttera pucherani and Agelastes meleagrides, are vaguely striped (rather blotchy) compared with the prominent striped patterns of guineafowl species that raise their chicks in grass, such as Numida meleagris and Acryllium vulturinum (Madge and McGowan 2002) (Fig. 2). The chick plumage of the forest-living A. niger is mainly dark rufous and black above (Little 2016).
Semi-striped: Grouse (Tetraonidae), Gallus gallus and Phasianus chicks have a variegated pattern with a central longitudinal band that proceeds through the crown to the forehead (Fig. 3). The rufous crown stripe often forms a single broad crown cap, with thinner trimmings on either side of the crown cap.
Striped: These chicks possess multiple stripes on the sides of their faces and are striped longitudinally across the crown right to the nares. Their back patterns are also variegated, but with a prominent central longitudinal band. Numida meleagris and A. vulturinum are typical examples of striped chicks (Fig. 2C, D). Coturnix coturnix chicks also display multiple stripes. The well-defined thin stripes across the crown and on the sides of the face of N. meleagris compared with the weakly defined stripes and blotches (fluidity) of A. meleagrides and G. pucherani suggest that the well-defined stripes emerged from a darkish plainer ancestor (see A. niger), with its black plain dorsal chick plumage. The latter three guineafowl species live in forests.
Chick plumage of spurfowl chicks
The 15 spurfowl chicks for which data were captured show a marked degree of similarity in terms of the selected character states (Table 3, Additional file 1: Table S1). The chick plumage of spurfowl chicks is regarded as semi-striped, since they lack the multiple disruptive stripes on the face and crown. The chick plumage of a hybrid P. adspersus and P. natalensis chick did not vary from this typical pattern. The back bears a broad, dark brown (rufous) central longitudinal band flanked by thinner and lighter-coloured stripes (otherwise known as a variegated back pattern). The crown has a broad rufous crown cap which is often trimmed by a thin, darker stripe on the edges. This crown cap is essentially an extension of the longitudinal band across the back. The face has an eye stripe which extends for a short distance in front of the eye (it often resembles a blotch in front of the eye). Some species, such as P. icterorynchus, P. nobilis and P. erckelii, generally have a reddish appearance, but their patterns (structurally) remain like the rest. P. hartlaubi is like the rest, with limited facial stripes and a variegated back pattern with a central longitudinal band on the back.
Chicks from two species showed prominent diagnostic features. Pternistis nobilis has a bold, thicker eye stripe, which is more prominent than the rest of the spurfowls, with a relatively thick frontal eye stripe. Pternistis erckelii has a solid, longish jaw stripe which in other species is faint or absent (Fig. 4).
Spurfowl chicks differ from their closest evolutionary relatives. Both the spurfowl chicks and Coturnix coturnix chicks are semi-striped on their heads but Alectoris chukar chicks possess stripes. Dorsally, only spurfowl chicks have a broad crown cap compared to scattered or banded crowns in the other two species (Table 3).
Chick plumage of francolin chicks
Data were captured for 11 species representing all four genera (Table 3).
Asiatic francolins: F. pondicerianus, F. francolinus and F. gularis are semi-striped. Like the spurfowls, they possess a rufous crown cap. The sides of their faces often have a few blotch-like blackish markings (probably remnants of stripes from an ancestor that was fully striped) behind the eye and on the neck. Like spurfowls, they also have a longitudinal band on the back with thinner, lighter-coloured lateral stripes (in other words, variegated back markings). Interestingly, only some F. pondicerianus chicks have a striped crown, showing intra-specific variability.
Dendroperdix sephaena is semi-striped, and shows resemblance to the spurfowls and Asiatic francolins. It has a rufous, crown cap with a solid eye line behind the eye, stretching down along the neck which is also typical for spurfowl chicks. It has a distinctive round dark spot on the neck, which it shares with F. francolinus and F. gularis (Fig. 5). The back also has a broad, dark brown central longitudinal band flanked with thinner, lighter-coloured stripes (in other words, variegated back markings) similar to spurfowl chicks.
The male P. coqui chick is semi-striped, with a rufous crown cap and a solid eye stripe behind the eye, a broad, dark brown longitudinal band on the back flanked by lighter lateral stripes reminiscent of spurfowl chicks (Fig. 6A, B). A female chick collected at Shangabue (Zimbabwe) shows a typical spurfowl crown and back, but the sides of the face have multiple stripes, which is typical of Scleroptila spp. (Fig. 6C). A similar female chick specimen is kept in the Ditsong National Museum of Natural History in South Africa. The distinction between female and male chicks is also evident at the juvenile stage, when the male has a clean buffy coloured face and the female multiple facial stripes; this is eventually carried through to adulthood. The male chicks resemble spurfowl chicks and are more closely related to the Asiatic chicks than to the striped chicks of Scleroptila spp.
Scleroptila gutturalis has a broad rufous crown cap, with multiple stripes on the face and a broad central longitudinal band on the back with thinner, light-coloured lateral stripes. Scleroptila levaillantii, S. shelleyi and S. afra have striped heads (instead of a well-defined crown cap) and facial markings, and the head colours are distinctively white and black, revealing a chevron pattern.
The Asiatic francolins, D. sephaena and the male P. coqui chick possess broad crown caps and semi-striped faces which are like their closest evolutionary relative G. gallus. Scleroptila species do not share these characteristics with G. gallus.
Chick plumage and Cytb phylogeny
The natal downy (Table 3) and Cytb data sets consisted of eight and 1,143 characters, consisting of eight and 430 parsimony informative characters, respectively. The matrices had a CI of 0.405, RI of 0.734 and HI of 0.595 whereas Cytb yielded a CI of 0.50, RI (of 0.521) and HI of 0.5, respectively. The Cytb phylogeny confirms the francolin-spurfowl dichotomy (Fig. 7) with francolins, spurfowls, grouse and allies (Tetraoninae) all in the family Phasianidae. Numididae is also recovered. The number of taxa included in this analysis had to match those for which the natal downy characters were available and this possibly could have resulted in the topology and nodal support that is slightly different from that in Crowe et al. (2006). The Asian/African linking lineage consisting of F. francolinus pondicerianus, F. gularis and D. sephana was recovered even though the branch from which these species arose is unresolved. The natal downy phylogeny (Fig. 8) shows poor phylogenetic structure which is largely polytomous and therefore no inferences can be made.
Symplesiomorphy underlying spurfowls
Ancestral characters form the “building blocks” that shape the colours and patterns of downy chicks. The broad longitudinal central rufous longitudinal band on the back and crown of spurfowl chicks (variegated) are also evident in G. gallus and grouse. The solid eye line of spurfowls, with the rest of the face often clean, is also evident in G. gallus, and is particularly similar between P. nobilis and G. gallus (see Figs. 3, 4). The prominent jaw stripe of P. erckelii (and to a lesser extent by other spurfowls) is also evident in Coturnix coturnix, N. meleagris and V. acryllium chicks.
Symplesiomorphy underlying francolins
The Asian francolins have a rufous central longitudinal band on the back and crown, like G. gallus. The blotches behind the eye (as in F. gularis) are like some Tetraonidae spp., being especially evident in D. obscurus pallides and L. lagopus. Dendroperdix sephaena has all the characteristics of the G. gallus chick. However, the single diagnostic isolated spot on the neck is similar to a spot recorded in the same area of the neck of F. gularis and F. francolinus (Fig. 5). Peliperdix coqui chicks also have the characteristics of G. gallus, but the female chick’s striped facial parts are similar to those of the N. meleagris chick. Scleroptila gutturalis falls in the same category as the female P. coqui chicks. It has a crown and back feather pattern like G. gallus, but the facial parts resemble N. meleagris chicks.
The chicks of S. afra, S. lavaillantii and S. shelleyi are similar to the striped pattern seen in N. meleagris, A. vulturinum and Coturnix coturnix chicks. However, the black lateral facial patterns of the latter three francolins stand out and could be related to the black facial parts of an Asiatic ancestor such as F. gularis. This is unlike S. gutturalis, which does not fall in this category and does not have black-coloured stripes. The plain colours of P. lathami chicks resemble the plain colours found in P. pucherani, A. meleagrides and A. niger.
Correlations between micro-habitat and chick plumage character states
Micro-habitat refers to the immediate environment of the bird within a broader landscape. Generally, species clades live in uniform micro-habitats for most of the year (Fig. 9). Some, such as N. meleagris and A. vulturinum live out in the open but breed in closed habitat, in other words in grass. Peliperdix lathami is an exception as it lives in forests but its close relatives, P. coqui and P. albogularis move into open micro-habitats (Fig. 9).
Most species that live in open micro-habitats (Peliperdix, Dendroperdix, Francolinus spp., Pternistis spp., L. lagopus, T. cupido and G. gallus) are semi-striped compared to Scleroptila spp., C. coturnix, N. meleagris and A. vulturinum that live in closed micro-habitats and are all multi-striped (more cryptic) (Additional file 1: Table S2). Most species that live in open micro-habitats possess rufous variegated colour combinations but species that live in closed micro-habitats have dark reddish and rufous colour combinations. Most forest species possess reddish colours (Additional file 1: Table S2).
Most species that live in open micro-habitats possess rufous caps on their crowns compared to all species living in closed micro-habitats that possess banded crowns. Forest species possess caps as well (Additional file 1: Table S2).
Most species that live in open micro-habitats possess a distinct eye band and comparatively most species that live in closed micro-habitats possess multiple facial stripes. Most forest species possess spots on the sides of their faces. Most species that live in open micro-habitats do not have jaw stripes whereas species that live in closed micro-habitats have partly or fully developed jaw stripes. Forest species do not possess any markings on the sides of their faces (Additional file 1: Table S2).
The back colours of species that live in open micro-habitats are rufous and most species that live in closed micro-habitats also possess rufous colours. Comparatively forest species possess dark reddish colours on their backs (Additional file 1: Table S2).
Most species that live in open micro-habitats possess broad stripes on their backs and species that live in closed micro-habitats possess thin and broad stripes. Comparatively forest species possess both but do not show any preference for any pattern (Additional file 1: Table S2).
Most species that live in open habitats possess no nose spots and for species that live in closed and forest habitats no preference was revealed. They both have spots or no spots. Generally, species of closed micro-habitats are more cryptic than species in open micro-habitats (Additional file 1: Table S2).
Ancestral state reconstruction
Disruptive markings
The ancestral state is inconclusive that is, the ancestor could have either been semi-striped or plain (with no markings). It seems semi-stripe is a plesiomorphic state among francolins and spurfowls with independent evolution of stripes in the grassland Scleroptila lineage, the spurfowls’ closest phylogenetic relative (Coturnix coturnix) and twice within Numididae and the sub-family Tetraoninae (Additional file 1: Fig. S2). There were two reversions to plain plumage in P. lathami and Tetrao urogallus.
Colour combinations of head
Generally, the ancestral states are inconclusive with the probability of all states (blackish brown, blackish, rufous variegated) having been present in the earlier ancestor. The colours of the head of M. maleo is plain black-brownish. This ancestral state together with the two diverged colour forms, rufous variegated and blackish colours, are found among the chicks of both Pternistis and Scleroptila spp. However, the head is consistently rufous variegated among Francolinus spp. (Additional file 1: Fig. S3).
Dorsal patterns
Generally, the ancestral states are inconclusive with the probability of all states (unchanged pail, banded, scattered, capped) having been present in the earlier ancestor. In M. maleo the dark head forms a continuous dark unchanged colour with the rest of the head and facial parts. The plain dorsal crown of M. maleo diverged into a well-defined capped crown found among Pternistis and Francolinus spp. but with a longitudinally banded pattern across the crown of Scleroptila species (Additional file 1: Fig. S4).
Side view patterns
The ancestral state is inconclusive, that is the ancestor may have had either plain or eye band/stripe. Francolins and spurfowls have eye band with independent evolution of multiple patterns in the grassland Scleroptila lineage and spots in the grouse and allies, Lagopus/Phasianus (Tetraoninae) lineage with an inconclusive ancestral state in members of Numididae. Unlike Scleroptila spp., the eye-stripes also evolved in Francolinus species (Additional file 1: Fig. S5).
Jaw stripe
With regard to this character, the ancestral state is plain (no distinguishable jaw stripe). Even though most of the deeper node states are inconclusive, the francolins and spurfowls generally have a plain state, the independent evolution of full (jaw stripe) occurred six times (thrice among francolins and once among spurfowls). The state “partly” stripe independently evolved one among francolins and twice among spurfowls. The grouse and allies is the lineage where the ancestral plain state persisted as well as in the linking lineage between Asian and African francolins (Additional file 1: Fig. S6).
Back colours
Generally, the ancestral states are inconclusive with the probability of all states (blackish-brown, blackish, rufous variegated) having been present in the earlier ancestor. The general back colour of the M. maleo chick is plain black-brownish. This ancestral character state plus a diverged rufous variegated pattern became characteristic among Pternistis spp. but Francolinus spp. only attained the rufous variegated patterns. Scleroptila spp. possess these variants but also include a blackish tone that is often revealed in the chicks of grouse and allies in the subfamily Tetraoninae. In short, all the ancestral states are consistently distributed across the tree. The exception if the independent evolution of a state shown by a white ball with black lines leading to a montane species P. castaneicollis and S. shelleyi which indicates that the observed state is undecided while the most parsimonious state is black brownish and rufous variegated, respectively (Additional file 1: Fig. S7).
Back patterns
Generally, the ancestral states are inconclusive with the probability of all states (plain, narrow, broad) having been present in the earlier ancestors. The M. maleo chick is black-brownish plain. This state diverged into two clear patterns. Most Pternistis spp. possesses a broad central back band flanked by two thinner but lighter coloured stripes (dilution of pigmentation) on either side. All Scleroptila spp. have markedly narrower back stripes which evolved independently and this is observed in P. rufopictus. Peliperdix lathami experienced a throw-back of plain colours on their backs as found in M. maleo. The re-appearance of plain back is also observed in T. cupido and A. meleagrides (Additional file 1: Fig. S8).
Nose spot
The ancestral state is plain (no distinguishable nose spot). Macrocephalon maleo does not possess a nose spot since the nose and crown consist of a continuous black-brownish plain colour. The absence of a nose spot prevails throughout the francolin and spurfowl lineage (pleisiomorphic state) with independent evolution of nose spots within the Red-winged grassland Scleroptila subclade, among spurfowls that is, among the Montane, Vermiculated species as well as in the most basal spurfowl species P. hartlaubi. Importantly, the plain state of ancestors such as M. maleo is due to full pigmentation while the plain state among francolin and spurfowl is due to the dilution of pigmentation (Additional file 1: Fig. S9).