Systematic Error in Seed Plant Phylogenomics

Resolving the closest relatives of Gnetales has been an enigmatic problem in seed plant phylogeny. The problem is known to be difficult because of the extent of divergence between this diverse group of gymnosperms and their closest phylogenetic relatives. Here, we investigate the evolutionary properties of conifer chloroplast DNA sequences. To improve taxon sampling of Cupressophyta (non-Pinaceae conifers), we report sequences from three new chloroplast (cp) genomes of Southern Hemisphere conifers. We have applied a site pattern sorting criterion to study compositional heterogeneity, heterotachy, and the fit of conifer chloroplast genome sequences to a general time reversible + G substitution model. We show that non-time reversible properties of aligned sequence positions in the chloroplast genomes of Gnetales mislead phylogenetic reconstruction of these seed plants. When 2,250 of the most varied sites in our concatenated alignment are excluded, phylogenetic analyses favor a close evolutionary relationship between the Gnetales and Pinaceae—the Gnepine hypothesis. Our analytical protocol provides a useful approach for evaluating the robustness of phylogenomic inferences. Our findings highlight the importance of goodness of fit between substitution model and data for understanding seed plant phylogeny

Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses

It has been suggested that the chloroplast genomes of the grass family, Poaceae, have undergone an elevated evolutionary rate compared to most other angiosperms, yet the details of this phenomenon have remained obscure. To know how the rate change occurred during evolution, estimation of the time-scale with reliable calibrations is needed. The recent finding of 65 Ma grass phytoliths in Cretaceous dinosaur coprolites places the diversification of the grasses to the Cretaceous period, and provides a reliable calibration in studying the tempo and mode of grass chloroplast evolution.By using chloroplast genome data from angiosperms and by taking account of new paleontological evidence, we now show that episodic rate acceleration both in terms of non-synonymous and synonymous substitutions occurred in the common ancestral branch of the core Poaceae (a group formed by rice, wheat, maize, and their allies) accompanied by adaptive evolution in several chloroplast proteins, while the rate reverted to the slow rate typical of most monocot species in the terminal branches.Our finding of episodic rate acceleration in the ancestral grasses accompanied by adaptive molecular evolution has a profound bearing on the evolution of grasses, which form a highly successful group of plants. The widely used model for estimating divergence times was based on the assumption of correlated rates between ancestral and descendant lineages. However, the assumption is proved to be inadequate in approximating the episodic rate acceleration in the ancestral grasses, and the assumption of independent rates is more appropriate. This finding has implications for studies of molecular evolutionary rates and time-scale of evolution in other groups of organisms

Phylogenomics and plant evolution : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Genetics at Massey University, Manawatu, New Zealand

Phylogenomics, the study of evolutionary relationships among groups of organisms using genome-scale data, is central to our understanding of the evolution of life. While large amounts of data are available and methodological developments are increasing at a fast pace, there are basic problems that are overlooked in phylogenomic analyses of molecular sequences, which may impede the accuracy and reliability of tree reconstruction. These problems include: How can we detect the non-phylogenetic signals from genomic data? How can we offer a better statistical fitness between the evolutionary model and data? How can we improve the phylogenetic inference using sophisticated and realistic models? How can we accurately infer the species trees? How can we quantitatively confirm the evolutionary theory? With these goals, this thesis concentrates on phylogenomics of land plants (and their origin) and evolution in general. • Resolving the phylogenetic position of Gnetales. We show that non-time reversible properties of positions in the chloroplast genomes of Gnetales mislead phylogenetic reconstruction, and highlight that the goodness of fit between substitution model and data should be taken into account when performing phylogenomic analyses. • Resolving the origin of land plants: 1). The multispecies coalescent model is applied to estimate the species tree of origin of land plants, and it is proved to be able to estimate accurate and congruent species tree in the presence of ancient incomplete lineage sorting from nuclear genes. 2). The chloroplast phylogenomic analyses are conducted using sophisticated and realistic evolutionary models that can account for site-heterogeneity and compositional heterogeneity. These chloroplast phylogenomic results confirm the previous nuclear data analyses. • We develop a statistical test and demonstrate that evolutionary theory could be tested by convergence of molecular data. It also indicates that the reality of evolution can be tested using standard methods and tools

The Origin of Land Plants: A Phylogenomic Perspective

Land plants are a natural group, and Charophyte algae are the closest lineages of land plants and have six morphologically diverged groups. The conjugating green algae (Zygnematales) are now suggested to be the extant sister group to land plants, providing the novel understanding for character evolution and early multicellular innovations in land plants. We review recent molecular phylogenetic work on the origin of land plants and discuss some future directions in phylogenomic analyses

Beyond reasonable doubt: evolution from DNA sequences.

We demonstrate quantitatively that, as predicted by evolutionary theory, sequences of homologous proteins from different species converge as we go further and further back in time. The converse, a non-evolutionary model can be expressed as probabilities, and the test works for chloroplast, nuclear and mitochondrial sequences, as well as for sequences that diverged at different time depths. Even on our conservative test, the probability that chance could produce the observed levels of ancestral convergence for just one of the eight datasets of 51 proteins is ≈1×10⁻¹⁹ and combined over 8 datasets is ≈1×10⁻¹³². By comparison, there are about 10⁸⁰ protons in the universe, hence the probability that the sequences could have been produced by a process involving unrelated ancestral sequences is about 10⁵⁰ lower than picking, among all protons, the same proton at random twice in a row. A non-evolutionary control model shows no convergence, and only a small number of parameters are required to account for the observations. It is time that that researchers insisted that doubters put up testable alternatives to evolution

We use two natural subgroups (X and Y), independently align the sequences for the species in each subgroup, independently determine the optimal tree for each subgroup, independently infer the ancestral sequences a_x and a_y on the optimal subtrees (in practice the sequence at the nearest node to the root of the subtree is estimated), and finally measure the pairwise alignment score between the ancestral sequences, s(a_x,a_y).

<p>Separately, we measure the alignment score between each pair of sequences (s(_i,j)) with one member in each of the two subsets, for example, s(_a,k), s(_a,l), s(_a,m), and so on.</p

SI_alignment_99_taxa_cp3

Alignment (in nexus format) of 3rd codon positions of 81 protein-coding chloroplast genes from 97 green plants and two red algae outgroup taxa

The Antarctic sea ice alga Chlamydomonas sp. ICE-L provides insights into adaptive patterns of chloroplast evolution

Abstract Background The ice alga Chlamydomonas sp. ICE-L is the main contributor to primary productivity in Antarctic sea ice ecosystems and is well adapted to the extremely harsh environment. However, the adaptive mechanism of Chlamydomonas sp. ICE-L to sea-ice environment remains unclear. To study the adaptive strategies in Chlamydomonas sp. ICE-L, we investigated the molecular evolution of chloroplast photosynthetic genes that are essential for the accumulation of carbohydrate and energy living in Antarctic sea ice. Results The 60 chloroplast protein-coding genes of Chlamydomonas sp. ICE-L were obtained, and the branch-site test detected significant signatures of positive selection on atpB, psaB, and rbcL genes in Chlamydomonas sp. ICE-L associated with the photosynthetic machinery. These positively selected genes were further identified as being under convergent evolution between Chlamydomonas sp. ICE-L and the halotolerant alga Dunaliella salina. Conclusions Our study provides evidence that the phototrophic component of Chlamydomonas sp. ICE-L exhibits adaptive evolution under extreme environment. The positive Darwinian selection operates on the chloroplast protein-coding genes of Antarctic ice algae adapted to extreme environment following functional-specific and lineages-specific patterns. In addition, three positively selected genes with convergent substitutions in Chlamydomonas sp. ICE-L were identified, and the adaptive modifications in these genes were in functionally important regions of the proteins. Our study provides a foundation for future experiments on the biochemical and physiological impacts of photosynthetic genes in green algae

SI_alignment_99_taxa_cp12

Alignment (in nexus format) of 1st and 2nd codon positions of 81 protein-coding chloroplast genes from 97 green plants and two red algae outgroup taxa