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The control region (CR) plays an important role in replication and transcription in the mitochondrial genome. Its supposedly high rate of DNA substitution makes it a suitable marker for studies of population and closely related species. Three domains can be identified in CR, each having its own characteristics regarding base composition, pattern of variability and rate of DNA substitution. We sequenced the complete CR for 27 cracids, including all 11 genera to characterize its molecular organization, describe patterns of DNA substitution along the gene, and estimate absolute rates of DNA substitution. Our results show that cracid CR organization and patterns of DNA substitution are typical of other birds. Conserved blocks C and B, fused CSB2/3, and a putative segment for bidirectional replication not usually present in birds were identified in cracids. We also suggest a new delimitation for domains to allow better comparisons among CRs at different taxonomic ranking. Our estimates of absolute rates of DNA substitution show that, in general, CR evolves at a rate slower than that of two protein-coding genes (CR, 0.14%-0.3%; ND2, 0.37%-0.47%; and cytochrome b, 0.29%-0.35% per site per million years within genera). Within CR domains, rates within genera ranged from 0.05% to 0.8% per site per million years.

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Alagoas Curassow Mitu mitu is considered extinct in the wild, having previously inhabited a small area in north-eastern Brazil that has since been replaced by sugar cane farms. Around 50 birds possessing morphological features of this species are still alive in captivity in Brazil, all being descendants from a breeding programme started in 1979, using offspring from a single male and two females captured from the wild. However, this captive population also includes some hybrids with the congeneric Razor-billed Curassow M. tuberosa and their descendants. Furthermore, the validity of Alagoas Curassow as a species is questionable. We used two molecular markers to study the validity of this taxon as a species, to detect potential hybrids present in the stock, and to estimate genetic variability among the remnant specimens. The analysis of 760 base pairs from mitochondrial cytochrome b and control region sequences revealed that at least three of the 20 birds analysed had sequences identical to those of Razor-billed Curassow. The other 17 birds presented sequences that diverged 2.6% from Razor-billed Curassow. Moreover, a sample from an Alagoas Curassow museum skin collected from the wild in 1951 had cytochrome b sequences identical to those of the 17 birds. These results confirm the Alagoas Curassow as a valid species. DNA fingerprinting profiles of the 20 descendants from the Alagoas Curassow breeding population showed that this group of birds is depauperate in genetic variability. There was an increase in genetic variability of birds born after 1990, attributed to the hybrid mating of Alagoas Curassow with Razor-billed Curassow. We suggest that birds born before 1990 should be handled separately from the others. However, if a decrease in chick harvest among birds of this group is detected due to inbreeding depression or ageing, cross-breeding between this group and the group of birds most closely related to it should be considered in order to enrich the progeny with the Alagoas Curassow genome.