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.

Peer Review #3 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.1)"

“…For these clades, there is sufficient phylogenetic signal in the three-gene datasets to robustly resolve relationships, and recovery of the same maximally supported clades in the plastome coding trees indicates there is either no conflict among plastome coding regions, or minimal conflict that does not affect support levels; the current data do not distinguish between these two possibilities. On the other hand, there is increased support for many clades in plastome coding trees compared to three-gene trees, consistent with our expectations and with results of earlier phylogenomic studies of grasses (Jones et al, 2014;Cotton et al, 2015;Saarela et al, 2015;Burke et al, 2016aBurke et al, , 2016bDuvall et al, 2016Duvall et al, , 2017Orton et al, 2016), confirming the utility of plastome phylogenomic studies for clarifying phylogenetic relationships at multiple hierarchical levels of the grass family. However, we also found some differences in resolution and support among three-gene and plastome coding trees.…”

“…Although at least one instance of conflict was identified among each of the 14 trees, conflicting clades (relative to the majority topology) were more common in trees derived from partitions including gapped sites, noncoding data or both. (Jones et al, 2014;Burke et al, 2016a;Orton et al, 2016). However, gapped sites may also be introduced in an alignment when portions of the plastome are difficult to align across divergent taxa, and poorly-aligned regions may represent noise in an analysis.…”

“…Warnow (2012) demonstrated, however, that ML analyses may be statistically inconsistent when gaps are treated as missing data (but see Truszkowski & Goldman, 2016), and other studies have similarly shown that treating gaps as missing data can result in incorrect tree topologies in varying phylogenetic contexts (Roure et al, 2013;Shavit Grievink et al, 2013;McTavish et al, 2015). Therefore, as an alternative treatment for another subset of analyses we removed possibly-ambiguously aligned nucleotides by Manuscript to be reviewed excluding all sites with a gap in at least one taxon (Jones et al, 2014;Cotton et al, 2015;Saarela et al, 2015;Attigala et al, 2016;Burke et al, 2016aBurke et al, , 2016bDuvall et al, 2016;Orton et al, 2016 overall plastome divergence, and branch support from noncoding data alone or when combined with coding data is sometimes stronger than from coding data for relationships among closelyrelated taxa (Ma et al, 2014;Saarela et al, 2015). (Christin et al, 2008a(Christin et al, , 2008b (Clark et al, 1995;Duvall et al, 2003Duvall et al, , 2007Grass Phylogeny Working Group II, 2012).…”

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

“… Saarela et al (2015) summarized all publications of grass plastomes published as of September 2014, and many new plastomes have since become available. Recent grass plastome sequences have been variously published in short contributions ( Myszczyński et al, 2015 ; Wang & Gao, 2015 , 2016 ; Lu et al, 2016 ; Perumal et al, 2016 ) or in the context of detailed phylogenomic analyses of different grass lineages, including the PACMAD clade ( Cotton et al, 2015 ; Teisher et al, 2017 ), Bambusoideae ( Wu et al, 2015 ; Wysocki et al, 2015 ; Attigala et al, 2016 ; Vieira et al, 2016 ; Zhang & Chen, 2016 ), Aristidoideae ( Besnard et al, 2014 ), Brachypodieae ( Sancho et al, 2017 ), early diverging grasses ( Burke et al, 2016a ), Panicoideae ( Burke et al, 2016b ), Chloridoideae ( Duvall et al, 2016 ), Zea ( Orton et al, 2017 ), Micrairoideae ( Duvall et al, 2017 ), Pooideae ( Saarela et al, 2015 ) and Oryzeae ( Kim et al, 2015 ; Liu et al, 2016 ; Wu & Ge, 2016 ; Zhang et al, 2016a , 2016b ). Phylogenomic analyses of plastomes have contributed increased resolution and support for many relationships within and among grass subfamilies compared with earlier single- and multi-gene plastid studies.…”

Phylogenomics and Plastome Evolution of Tropical Forest Grasses (Leptaspis, Streptochaeta: Poaceae)

“…These events, which are called rare genomic changes (RGC) in recent studies of grass plastomes (Jones et al, 2014; Duvall et al, 2016; Orton et al, 2016), are distinguished not only by relative infrequency, but can also be attributed to mutational processes that distinguish them from microstructural changes such as non-reciprocal site-specific recombinations (Graur and Li, 2000). Morris and Duvall (2010) presented a detailed comparison of plastome structure in Anomochloa marantoidea to those of other grasses.…”