This chapter rehearses the argument made throughout the book: the natural world, though full of suffering and violence, is not fallen. Instead, the evolutionary process is the result of God, in love, allowing the creation to “selve” even in ways that bring harm. God does not leave the creation in this state, but accompanies and works with creatures and events to redeem suffering in both this-worldly and other-worldly ways.

Phylogenetic relationships within the green algal phylum Chlorophyta have proven difficult to resolve. The core Chlorophyta include Chlorophyceae, Ulvophyceae, Trebouxiophyceae, Pedinophyceae and Chlorodendrophyceae, but the relationships among these classes remain unresolved and the monophyly of Ulvophyceae and Trebouxiophyceae are highly controversial. We analyzed a dataset of 101 green algal species and 73 protein-coding genes sampled from complete and partial chloroplast genomes, including six newly sequenced ulvophyte genomes (Blidingia minima NIES-1837, Ulothrix zonata, Halochlorococcum sp. NIES-1838, Scotinosphaera sp. NIES-154, Caulerpa brownii and Cephaleuros sp. HZ-2017). We applied the Tree Certainty (TC) score to quantify the level of incongruence between phylogenetic trees in chloroplast genomic datasets, and show that the conflicting phylogenetic trees of core Chlorophyta stem from the most GC-heterogeneous sites. With removing the most GC-heterogeneous sites, our chloroplast phylogenomic analyses using heterogeneous models consistently support monophyly of the Chlorophyceae and of the Trebouxiophyceae, but the Ulvophyceae was resolved as polyphyletic. Our analytical framework provides an efficient approach to reconstruct the optimal phylogenetic relationships by minimizing conflicting signals.

We need to estimate protein tertiary structure, as well as using primary sequences, in order to further our understanding of protein evolution and evolutionary processes in general.

Green plants comprise two main clades: the Streptophyta, which include charophyte green algae and the embryophytic land plants, and the Chlorophyta including a wide diversity of marine, freshwater, and terrestrial green algae. Establishing a robust phylogeny is important to provide an evolutionary framework for comparative and functional studies. During the last two decades our understanding of the evolution of green algae has profoundly changed, first by phylogenetic analyses of nuclear ribosomal sequence data (mainly 18S), and more recently by analyses of multi-gene and chloroplast genomic data. The phylogenetic relationships among the main streptophytan lineages have been extensively studied and are now relatively well resolved. Although a lot of progress has been made in the last few years, the phylogenetic relationships in the Chlorophyta are still less well established. Here we review how chloroplast genomic data have contributed to address relationships among the main chlorophytan lineages. We highlight recent progress and conflicts among different studies, and discuss future directions in chloroplast phylogenomics of green algae.

Competing hypotheses seek to explain the evolution of oxygenic and anoxygenic processes of photosyn- thesis. Since chlorophyll is less reduced and precedes bacte- riochlorophyll on the modern biosynthetic pathway, it has been proposed that chlorophyll preceded bacteriochlorophyll in its evolution. However, recent analyses of nucleotide se- quences that encode chlorophyll and bacteriochlorophyll bio- synthetic enzymes appear to provide support for an alterna- tive hypothesis. This is that the evolution of bacteriochloro- phyll occurred earlier than the evolution of chlorophyll. Here we demonstrate that the presence of invariant sites in se- quence datasets leads to inconsistency in tree building (in- cluding maximum-likelihood methods). Homologous se- quences with different biological functions often share invari- ant sites at the same nucleotide positions. However, different constraints can also result in additional invariant sites unique to the genes, which have specific and different biological functions. Consequently, the distribution of these sites can be uneven between the different types of homologous genes. The presence of invariant sites, shared by related biosynthetic genes as well as those unique to only some of these genes, has misled the recent evolutionary analysis of oxygenic and an- oxygenic photosynthetic pigments. We evaluate an alternative scheme for the evolution of chlorophyll and bacteriochloro-

In a recent article published in these pages, Bowman and colleagues propose that the ribosome represents a challenge to the RNA world model, a long-standing framework to explain the origin of DNA and genetically encoded proteins from a hypothetical RNA-based system. Specifically, they outline a scenario for the emergence and subsequent coevolution of the peptidyl transferase centre (PTC) of the ribosome with non-templated peptide products of this RNA through chemical evolution. They also propose that the PTC would have predated the emergence of enzymatic RNA replication, and that this in turn indicates that the RNA world never existed. We and others have previously incorporated non-templated peptide production as an early stage in the evolution of protein synthesis, which we would count as a chemical process, in agreement with Bowman and colleagues' model. However, their model raises an important question: to what extent could early protein synthesis and its products have evolved in the absence of Darwinian processes? We argue that evolution of the early ribosome requires Darwinian evolution, and that, while chemical evolution could give rise to peptidyl transferase activity, it is insufficient for subsequent improvement of a proto-PTC, or for ongoing coevolution of the proto-PTC with its early non-templated peptide products. We conclude that it is difficult to preclude the involvement of replicative processes, themselves subject to Darwinian evolution, from the evolution of the PTC. Finally, Bowman et al. call into question current models for the RNA to protein transition. We show that the difficulty that Bowman et al. have with this scenario is down to a misreading of our previous work.

The green algal phylum Chlorophyta has six diverse classes, but the phylogenetic relationship of the classes within Chlorophyta remains uncertain. In order to better understand the ancient Chlorophyta evolution, we have applied a site pattern sorting method to study compositional heterogeneity and the model fit in the green algal chloroplast genomic data. We show that the fastest-evolving sites are significantly correlated with among-site compositional heterogeneity and these sites have a much poorer fit to the evolutionary model. Our phylogenomic analyses suggest that the class Chlorophyceae is a monophyletic group and the classes Ulvophyceae, Trebouxiophyceae and Prasinophyceae are non-monophyletic groups. Our proposed phylogenetic tree of Chlorophyta will offer new insights to investigate ancient green algae evolution and our analytical framework will provide a useful approach for evaluating and mitigating the potential errors of phylogenomic inferences.

Perhaps the 'selfish' aspect of evolution has been over-emphasised, and organisms considered as basically selfish. However, at the macromolecular level of genes and proteins the cooperative aspect of evolution is more obvious and balances this self-centred aspect. Thousands of proteins must function together in an integrated manner to use and to produce the many molecules necessary for a functioning cell. The macromolecules have no idea whether they are functioning cooperatively or competitively with other genes and gene products (such as proteins). The cell is a giant cooperative system of thousands of genes/proteins that function together, even if it has to simultaneously resist 'parasites'. There are extensive examples of cooperative behavior among genes and proteins in both functioning cells and in the origin of life, so this cooperative nature, along with selfishness, must be considered part of normal evolution. The principles also apply to very large numbers of examples of 'positive interactions' between organisms, including both eukaryotes and akaryotes (prokaryotes). This does not negate in any way the 'selfishness' of genes – but macromolecules have no idea when they are helping, or hindering, other groups of macromolecules. We need to assert more strongly that genes, and gene products, function together as a cooperative unit. Reviewers: This article was reviewed by Prof. Bill Martin (Düsseldorf), Dr. Nicolas Galtier (Montpellier) and Dr. Anthony Poole (Christchurch).

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.

It is not really helpful to consider modern environmental epigenetics as neo-Lamarckian; and there is no evidence that Lamarck considered the idea original to himself. We must all keep learning about inheritance, but attributing modern ideas to early researchers is not helpful, and can be misleading.

Two basic questions are considered that approach protein evolution from different directions; the problems arising from using Markov models for the deeper divergences, and then the origin of proteins themselves. The real problem for the first question (going backwards in time) is that at deeper phylogenies the Markov models of sequence evolution must lose information exponentially at deeper divergences, and several testable methods are suggested that should help resolve these deeper divergences. For the second question (coming forwards in time) a problem is that most models for the origin of protein synthesis do not give a role for the very earliest stages of the process. From our knowledge of the importance of replication accuracy in limiting the length of a coding molecule, a testable hypothesis is proposed. The length of the code, the code itself, and tRNAs would all have prior roles in increasing the accuracy of RNA replication; thus proteins would have been formed only after the tRNAs and the length of the triplet code are already formed. Both questions lead to testable predictions.

Passerines are the largest avian order, and the 6,000 species comprise more than half of all extant bird species. This successful radiation probably had its origin in the Australasian region, but dating this origin has been difficult due to a scarce fossil record and poor biogeographic assumptions. Many of New Zealand's endemic passerines fall within the deeper branches of the passerine radiation, and a well resolved phylogeny for the modern New Zealand element in the deeper branches of the oscine lineage will help us understand both oscine and passerine biogeography. To this end we present complete mitochondrial genomes representing all families of New Zealand passerines in a phylogenetic framework of over 100 passerine species. Dating analyses of this robust phylogeny suggest Passeriformes originated in the early Paleocene, with the major lineages of oscines "escaping" from Australasia about 30 Ma, and radiating throughout the world during the Oligocene. This independently derived conclusion is consistent with the passerine fossil record.

AimWe used endemic frogs to test the hypothesis that New Zealand was fully submerged during the Oligocene marine transgression (c. 25-35Ma, the Oligocene drowning) and that all the land biota subsequently arrived by dispersal - including the poorly dispersing frogs.LocationNew Zealand.MethodsThe complete mitochondrial genome of the New Zealand native frog Leiopelma hochstetteri was sequenced, assembled and analysed, and compared with that of L. archeyi.ResultsUsing many phylogenetic analyses we examined the evolutionary relationships of the two species of Leiopelma, both for the deepest divergence within New Zealand and relative to other frogs. Our results give estimates of well over 65Ma for the first divergence of leiopelmatid frogs within New Zealand, and over 150Ma for the divergence of Leiopelma from its closest relative, the North American tailed frog Ascaphus truei.Main conclusionsThe identification of such a deep divergence among the extant Leiopelma species provides some of the strongest support yet for a mixed-age model for the origin of New Zealand's terrestrial biota, where some elements are of vicariant origin and others have arisen by long-distance dispersal. This contradicts a full drowning model and supports the view that there must have been some continuous land through the Oligocene.

Early evolutionary thinkers proposed relatively simple models to describe processes of evolution, and these are the basis of evolutionary models still used today. Recent research has since shown that evolutionary relationships among plants can be complex and difficult to reconstruct even from molecular data. In plants there is a continuum of processes, ranging from reticulate relationships within a sexually reproducing population, incomplete lineage sorting and hybridization between recently diverged species, allopolyploidy between more distantly related species, to symbioses and endosymbiosis. These aspects of plant biology can create practical problems for interpreting bifurcating gene trees and identifying species. The promise of "omics" is that it will provide data and analyses to improve our understanding of the nature of species and their phylogenetic relationships. We highlight the importance of distinguishing evolutionary processes and evolutionary models, and stress that improving the understanding of micro-evolutionary processes is necessary to inform current debate on whether or not to accept paraphyletic species.

We report three new avian mitochondrial genomes, two from widely separated groups of owls and a falcon relative (the Secretarybird). We then report additional progress in resolving Neoavian relationships in that the two groups of owls do come together (it is not just long-branch attraction), and the Secretarybird is the deepest divergence on the Accipitridae lineage. This is now agreed between mitochondrial and nuclear sequences. There is no evidence for the monophyly of the combined three groups of raptors (owls, eagles, and falcons), and again this is agreed by nuclear and mitochondrial sequences. All three groups (owls, accipitrids [eagles], and falcons) do appear to be members of the "higher land birds," and though there may not yet be full "consilience" between mitochondrial and nuclear sequences for the precise order of divergences of the eagles, falcons, and the owls, there is good progress on their relationships.

Springer and Gatesy [1] give a slightly different hypothesis of the origin of land plants but suggest both that their results 'undermine major conclusions' in our paper [2] and that the coalescent model is not reliable for deep phylogenetic questions such as the origin of land plants. There are three aspects to our response: (i) there are important points of agreement between the two studies (the biological aspect); (ii) the trees obtained by the two studies are very similar (the mathematical aspect); and (iii) there are differences between the methods used (the computational aspect).