title: Plastid phylogenomic study of species within the genus Zea: rates and patterns of three classes of microstructural changes.
abstract: This project examines the relationships within the genus Zea using complete plastid genomes (plastomes). While Zea mays has been well studied, congeneric species have yet to be as thoroughly examined. For this study four complete plastomes and a fifth nearly complete plastome were sequenced in the five species (Zea diploperennis, Zea perennis, Zea luxurians, Zea nicaraguensis, and Zea mays subsp. huehuetenangensis) by Sanger or next-generation methods. An analysis of the microstructural changes, such as inversions, insertion or deletion mutations (indels) and determination of their frequencies were performed for the complete plastomes. It was determined that 193 indels and 15 inversions occurred across the examined plastomes of Zea. Tandem repeat indels were the most common type of microstructural change observed. Divergence times were estimated using a noncorrelated relaxed clock method. Divergence dates for specific nodes relative to Zea were calculated to fall between 38,000 years before present (YBP) for the subspecies included in this study and 23,000 YBP for section Luxuriantes included in this study. The stem lineage of all Zea species was calculated to have diverged at 176,000 YBP. The calculated mutation rates for the genus fell within the range of 1.7E-8 to 3.5E-8 microstructural changes per site per year. These rates of change are not uniform, despite the close relationships of taxa in this study. Phylogenomic analyses using full plastome alignments were also conducted to compare tree topologies from different types of mutations. In most cases, the previous work examining Zea mitochondrial and nuclear data was confirmed.
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, Dekalb, IL, 60115-2861, USA. lauren.orton@outlook.com.
authors.forename: Lauren M
authors.initials: LM
authors.lastname: Orton
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, Dekalb, IL, 60115-2861, USA.
authors.forename: Sean V
authors.initials: SV
authors.lastname: Burke
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, Dekalb, IL, 60115-2861, USA.|University of Chicago, Center for Data Intensive Sciences, 5454 S. Shore Dr., Chicago, IL, 60615, USA.
authors.forename: William P
authors.initials: WP
authors.lastname: Wysocki
authors.affiliation: Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, Dekalb, IL, 60115-2861, USA.
authors.forename: Melvin R
authors.initials: MR
authors.lastname: Duvall
mesh_terms: D001483:Base Sequence; D018742:DNA, Chloroplast / Q000737:chemistry / Q000235:genetics*; D014644:Genetic Variation; D054627:Genome, Plastid / Q000235:genetics*; D009154:Mutation; D059645:Mutation Rate; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D013045:Species Specificity; D013997:Time Factors; D003313:Zea mays / Q000145:classification / Q000235:genetics*
chemical_list: D018742:DNA, Chloroplast
keywords: Evolutionary divergence; Grasses; Microstructural changes; Phylogeny; Plastid; Zea