Introduction

In the following, an alignment of nucleobases of the control region of selected species of the superorder Galloanserae is provided. Nucleobases that could be aligned with reasonable certainty are highlighted by various colours. Potential apomorphies are highlighted in red, while convergent nucleobase substitutions are highlighted in yellow. 

Aligned partial control region sequences of thirty selected species of Galloanserae. Eleven unalignable regions (U-1 to U-11) and elven alignable regions (A-1 to A-11) are distinguished, with only the elongate terminal unalignable region (U-12) not being represented. [Colour symbols: dark blue for "G", light blue for "A", dark green for "T", light green for "C", pink for nucleotide transitions, purple for nucleotide transversions, orange for mixed transitions/ transversions, black for unresolved anseriform/galliform ground-pattern apomorphies, red for apomorphies in general, yellow for convergences, grey for deletions, and brown for insertions of varying lengths that are indicated by numbers]

As can be seen from the above sequences, the alignment is not always straightforward, and different regions vary with respect to alignability. Whenever multiple indels occur in variable regions, alignability is immediately lost. On the other hand, there are several conserved regions where only a limited number of nucleotide substitutions are encountered. A schematic map of the control region of Galloanserae is given below in order to provide an overview of the observed distribution of alignable and unalignable regions: 

Schematic map of the control region in Galloanserae, with unalignable regions (U-1 to U-12) and alignable regions (A-1 to A-11) being distinguished. For comparison, the traditionally recognised domains and conserved boxes are presented in colour below. [Note that some of the alignable regions (e.g. A-2, A-7, A-8, A-9, as well as parts of A-5 and A-10) are lacking a corresponding traditional conserved box although no base substitutions were observed in Galloanserae]

Taken together, the control region exhibits a remarkable mix of variable and conserved regions. Because only the conserved regions are alignable, the control region turned out to be particularly informative in resolving phylogenetic relationships at the family level: 

List of control-region apomorphies mapped onto the phylogeny of Galloanserae. While some relationships are particularly well resolved, others lack support altogether. Overall, the degree of homoplasy is limited, but some convergencies are encountered (summarised in the yellow box). Most parallelisms are easily recognised, because they are outnumbered by true apomorphies. Note that basal relationships within Galliformes (landfowl) and Anseriformes (waterfowl), respectively, are not shown, as there were no Struthioniformes or Neoaves included as outgroups. 

One finding deserves particular consideration: from nuclear studies we know that screamers (Anhimidae) represent the basalmost family of waterfowl, and that magpie-geese (Anseranatidae) diverge next (Prum et al., 2015; Kuhl et al., 2021). These results are corroborated by morphological data (Livezey, 1986). Therefore, it is very surprising to find that control-region sequences provide strong evidence (by 11 apomorphies) for a sister-group relationship between these two families. In other cases of mito-nuclear discordance, inconsistencies among different data sets are usually attributed to incomplete lineage sorting and/or introgression as a result of hybridisation. However, because of the mere amount of conflicting data, in this particular case the hybridising species must have belonged to different families. Are viable hybrid offspring really to be expected under these conditions?

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