Gallus gallus aggrecan gene-based phylogenetic analysis of selected avian taxonomic groups

Abstract

Mitochondrial DNA (mtDNA) sequences remain the most widely used for phylogenetic analysis in birds. A major limitation of mtDNA sequences, however, is that mitochondria genes are inherited as a single linkage group. Here we describe the use of a 540-bp DNA sequence corresponding to the G3 domain of Gallus gallus nuclear aggrecan gene (AGCI) for phylogenetic analysis of the main groups of Galliformes including Phasianidae, Numididae, and Odontophoridae. We also included species from Cracidae and Megapodiidae which are considered by some as Craciformes and others, including here as Galliformes. The uncorrected sequence divergence of the G3 fragments ranges from 1% among the grouses to 36% between some of the distant groups within Galliformes. These sequences contain 39-48% AT nucleotides and the ratios of transition versus transversion are above 1.5 in majority of the comparisons. Using G3 sequences from an Anseriform, Oxyura jamaicensis, as out-groups, phylogenetic trees were obtained using maximum parsimony and distance algorithms and bootstrap analyses. These trees were consistent with those described using Avian sarcoma and leucosis virus gag genes and those from amino acid sequences of hemoglobin and lysozyme c. Our data also support relationships among Galliformes which were defined using mtDNA sequences. In addition to the general support of the five main families of Galliformes, our data are also consistent with previous work that showed Francolinus africanus and Gallus gallus are in the same clade and that Tetraoninae is a well-supported monophyletic subfamily within Phasianidae. The results presented here suggest that the AGC1 sequences meet the criterion of novel nuclear DNA sequences that can be used to help resolve the relationships among Galliformes.

CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes)

“…Discrepancies about the phylogenetic position of G. gallus based on various morphological, behavioral, and molecular methodologies have been noted in previous studies (Bonilla et al, 2010;Bush and Strobeck, 2003;Crowe et al, 2006;Dyke et al, 2003;Kaiser et al, 2007;Kimball and Braun, 2008;Lucchini and Randi, 1999;Shen et al, 2010;Smith et al, 2005). Some studies support the conclusions in this paper that G. gallus should be placed as a basal member of the Phasianidae (Bush and Strobeck, 2003;Kaiser et al, 2007;Kriegs et al, 2007).…”

“…This group then formed a paraphyletic assemblage of other Phasianidae birds. Nearly all subsequent studies based on nucleotide sequence data from mitochondrial gene regions and nuclear genes (e.g., the CYT B, NADH2, 3′-UTR, Ovomucoid, Aldolase b, and the combined data) support this opinion (Bonilla et al, 2010;Kimball and Braun, 2008;Meng et al, 2010;Shen et al, 2010;Smith et al, 2005). This was also consistent with morphological cladistic analysis (Dyke et al, 2003) and the combined data including morphological and molecular data (Crowe et al, 2006).…”

Avian Genomes: Important Resources for Understanding Vertebrate Biology

“…Polymerase chain reaction (PCR) primers designed using chicken CR1 were tested on different avian species including guinea fowl and turkey. Consistent with phylogenetic relationships described elsewhere (25), the primers amplified single fragments only in the guinea fowl, but not in the turkey and quail, more distantly related species. For the turkey, multiple fragments were obtained at annealing temperatures ranging from 48 to 60 C.…”

“…They may also provide a resource for analyzing other avian genomes as well as for evaluating relatedness among birds. Recently, for example, we used Gallus gallus aggrecan to conduct a phylogenetic assessment of relatedness among 48 avian species [25]. The analysis, which supported mitochondria DNA and retroviral evaluations, provides a novel nuclear locus with strong phylogenetic signal.…”

Identification of New World Quails Susceptible to Infection with Avian Leukosis Virus Subgroup J

“…The topology corroborates previously published data that place guinea fowl and New World quails, belonging to the families Numididae and Odontophoridae, respectively, outside of the monophyletic Phasianidae. Within the family Phasianidae, the branching pattern is mostly in accordance with those of phylogenetic trees based on mitochondrial sequences, nuclear sequences, or CR1 insertions (29)(30)(31). Our topology does not support the monophyly of the subfamily Phasianinae, because Reeves's pheasant groups with chicken, and ring-necked pheasant groups with turkey.…”