TY - JOUR
T1 - Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes
AU - Schirtzinger, Erin E.
AU - Tavares, Erika S.
AU - Gonzales, Lauren A.
AU - Eberhard, Jessica R.
AU - Miyaki, Cristina Y.
AU - Sanchez, Juan J.
AU - Hernandez, Alexis
AU - Müeller, Heinrich
AU - Graves, Gary R.
AU - Fleischer, Robert C.
AU - Wright, Timothy F.
N1 - Funding Information:
We thank the following institutions and people for the generous loan of tissue specimens: American Museum of Natural History (P. Sweet), Academy of Natural Sciences of Philadelphia (L. Joseph), the African Safari Zoo, the Australian National Wildlife Collection (L. Joseph), the Field Museum of Natural History (D. Willard), Fundação Crax, University of Kansas Museum of Natural History (M. Robbins), Loro Parque Fundación, Louisiana State University Museum of Natural Science (R. Brumfield), Museu Paraense Emílio Goeldi, Parque Ecológico do Tietê, the San Diego Zoological Park (N. Lamberski), Universidade Estadual Paulista (UNESP), the US National Museum of Natural History, the New Mexico State University Vertebrate Museum (P. Houde), Zoológico de Sorocaba, Zoológico de Americana, Zoológico Cyro-Gevaerd and several breeders. We particularly thank David Waugh, Sara Cappelli and Julia Scharpegge of the Loro Parque Fundación and Tania Matsumoto for generous assistance in obtaining data from critical specimens. We thank Rogério Lourenço for providing some of the sequences, Sergio L. Pereira for suggestions, and Elizabeth Moseman for many useful comments on the manuscript. Research support was provided by NIH grant S06 GM008136 (TFW), Sigma Xi Grant-in-Aid-of-Research (EES), Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) (EST), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (EST) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (EST). CYM has a CNPq research productivity fellowship. This study was approved by the Institutional Animal Care and Use Committee of New Mexico State University.
PY - 2012/8
Y1 - 2012/8
N2 - Mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Aves). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and mapped these states onto the phylogeny. We further sequenced 44 selected species to validate these inferences of control region state. Ancestral state reconstruction using a range of weighting schemes identified six independent origins of mitochondrial control region duplications within Psittaciformes. Analysis of sequence data showed that varying levels of mitochondrial gene and tRNA homology and degradation were present within a given clade exhibiting duplications. Levels of divergence between control regions within an individual varied from 0-10.9% with the differences occurring mainly between 51 and 225 nucleotides 3' of the goose hairpin in domain I. Further investigations into the fates of duplicated mitochondrial genes, the potential costs and benefits of having a second control region, and the complex relationship between evolutionary rates, selection, and time since duplication are needed to fully explain these patterns in the mitochondrial genome.
AB - Mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Aves). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and mapped these states onto the phylogeny. We further sequenced 44 selected species to validate these inferences of control region state. Ancestral state reconstruction using a range of weighting schemes identified six independent origins of mitochondrial control region duplications within Psittaciformes. Analysis of sequence data showed that varying levels of mitochondrial gene and tRNA homology and degradation were present within a given clade exhibiting duplications. Levels of divergence between control regions within an individual varied from 0-10.9% with the differences occurring mainly between 51 and 225 nucleotides 3' of the goose hairpin in domain I. Further investigations into the fates of duplicated mitochondrial genes, the potential costs and benefits of having a second control region, and the complex relationship between evolutionary rates, selection, and time since duplication are needed to fully explain these patterns in the mitochondrial genome.
KW - Ancestral state reconstruction
KW - Control region
KW - Control region duplication
KW - Gene duplication
KW - Mitochondrial genomes
KW - Parrots
UR - http://www.scopus.com/inward/record.url?scp=84861528682&partnerID=8YFLogxK
U2 - 10.1016/j.ympev.2012.04.009
DO - 10.1016/j.ympev.2012.04.009
M3 - Article
C2 - 22543055
AN - SCOPUS:84861528682
SN - 1055-7903
VL - 64
SP - 342
EP - 356
JO - Molecular Phylogenetics and Evolution
JF - Molecular Phylogenetics and Evolution
IS - 2
ER -