Phylogeny and evolution of cranes (Aves: Gruidae) inferred from DNA sequences of multiple genes

The phylogeny of cranes (Aves: Gruidae) has been intensively studied and has resulted in a clear picture of the pattern of evolutionary diversification within this avian family. However, some aspects of crane relationships remain unresolved. In this research, I studied the phylogeny of cranes inferred from sequences of the mitochondrial genes for the control region and the glutamic acid tRNA, and combined those with sequences from the genes for cytochrome b, NADH dehydrogenase subunit 6, the threonine tRNA and the proline tRNA. I also sequenced part of an independent nuclear locus, the seventh intron of the β-fibrinogen gene to test the estimate from the mitochondrial sequence data. Analyses of these data under various phylogenetic methods are fully congruent with previous estimates of crane phylogeny and demonstrate the utility of information from the control region in resolving close relationships involved in rapid successive speciation events. Analysis of the nuclear-intron was congruent with trees estimated from mitochondrial DNA data, but not well-resolved, raising the question of whether nuclear sequences will be of general utility in addressing relationships among recently evolved taxa. Application of different models demonstrate that crane phylogeny is largely resistant to changes in underlying assumptions regarding the process of sequence evolution. However, the “best” models for each partition of the data indicate heterogeneity in transition bias, relative rates, and nucleotide composition within and between genes. Taking these factors into account does not appear to improve, nor decrease, the accuracy or precision of estimated phylogenies, although the precision and accuracy of parameter estimation may be negatively affected as model complexity increases. The inferred root of the gruine tree is particularly sensitive to differing model assumptions for the mitochondrial sequence data, and either represents a case where simpler models are providing a more accurate answer, or perhaps is an example of method inconsistency. Simulation tests and congruence with previous studies indicate that the former is more likely in this instance. The resulting crane phylogeny provides a framework within which to conduct interspecific comparative studies of the historical processes leading to present-day diversity in biological traits. I examined hypotheses for the adaptive evolution of the elongated trachea and associated sternal morphology found in gruine cranes using the most current phylogeny and phylogenetically independent contrasts correlation methods. Acoustic explanations are better-developed and appear more plausible for tracheal elongation in general, but physiologic selective advantages for the particular extreme morphological modification of crane tracheae could not be adequately tested, and should not be ruled out.