A review paper about very plastic repertories of the regulatory genes in vertebrate genomes (Nodal and Lefty) has been published in the journal Developmental Dynamics.
Enigmatic Nodal and Lefty gene repertoire discrepancy: Latent evolutionary history revealed by vertebrate-wide phylogeny
This review will be a part of the special issue 'The Establishment, Maintenance and Breaking of Symmetry'. It would be great to see other articles building up this species issue.
One symbolic figure from this review has been pasted below. Previously, the mouse and chicken Nodal genes (retained as a single copy in each of the genomes) were regarded as orthologous to each other, but they later turned out not to be.
In the paralogy recognition, particularly remarkable was the identification of the two anole Nodal genes in the figure. I remember Christophe Dessimoz called this sort of gene retention 'witness of non-orthology'. The Nodal genes provided a typical model case illustrating it.
See Kuraku and Kuratani 2011 for more cases of gene loss (than Nodal2) in the mammalian lineage, Kajikawa et al. 2021 for differential mechanisms of left-right symmetry breaking in early mammalian development involving Nodal genes, and Kuraku 2010 for more episodes of hidden paralogy among vertebrate genes.