Proterozoic photosynthesis – a critical review

Chlorophyll‐based photosynthesis has fuelled the biosphere since at least the early Archean, but it was the ecological takeover of oxygenic cyanobacteria in the early Palaeoproterozoic, and of photosynthetic eukaryotes in the late Neoproterozoic, that gave rise to a recognizably modern ocean–atmosphere system. The fossil record offers a unique view of photosynthesis in deep time, but is deeply compromised by differential preservation and non‐diagnostic morphologies. The pervasively polyphyletic expression of modern cyanobacterial phenotypes means that few Proterozoic fossils are likely to be members of extant clades; rather than billion‐year stasis, their similarity to modern counterparts is better interpreted as a combination of serial convergence and extinction, facilitated by high levels of horizontal gene transfer. There are few grounds for identifying cyanobacterial akinetes or crown‐group Nostocales in the Proterozoic record. Such recognition undermines the results of various ancestral state reconstruction analyses, as well as molecular clock estimates calibrated against demonstrably problematic Proterozoic fossils. Eukaryotic organisms are likely to have acquired their (stem‐group nostocalean) photoendosymbionts/plastids by at least the Palaeoproterozoic, but remained ecologically marginalized by incumbent cyanobacteria until the late Neoproterozoic appearance of suspension‐feeding animals.     

Phylogenomic Analysis of the α Proteasome Gene Family from Early-Diverging Eukaryotes

We employed a phylogenomic approach to study the evolution of α subunits of the proteasome gene family from early diverging eukaryotes. BLAST similarity searches of the Giardia lamblia genome identified all seven α proteasome genes characteristic of eukaryotes from the crown group. In addition, a PCR strategy for the amplification of multiple α subunit sequences generated single α proteasome products for representatives of the Kinetoplastida (Leishmania major), the Parabasalia (Trichomonas vaginalis), and the Microsporidia (Vairimorpha sp., Nosema sp., Endoreticulata sp., and Spraguea lophii). The kinetoplastid Trypanosoma cruzi and the eukaryote crown group Acanthamoeba castellanii yielded two distinct α proteasome genes each. The presence of seven distinct α proteasome genes in G. lamblia, one of the earliest-diverging eukaryotes, indicates that the α proteasome gene family evolved rapidly from a minimum of one gene in Archaea to seven or more in Eukarya. Results from the phylogenomic analysis are consistent with the idea that the Diplomonida (as represented by G. lamblia), the Kinetoplastida, the Parabasalia, and the Microsporidia diverged after the duplication events that originated the α proteasome gene family. A model for the early origin and evolution of the proteasome gene family is presented. Received: 14 February 2000 / Accepted: 14 August 2000     

The evolution of aquatic feeding in seals: insights from Enaliarctos (Carnivora: Pinnipedimorpha), the oldest known seal

The development of pierce‐feeding and loss of oral processing represented major adaptations for underwater feeding in marine mammals. We examined the evolution of pierce‐feeding and its association with changes in tooth spacing and tooth size to determine whether pierce‐feeding was practiced by the earliest known pinnipeds. Data on crown size and spacing in postcanine dentition were collected and 1) analysed by principal components analysis (PCA) to determine the tooth morphospace of arctoid carnivores, 2) analysed by least squares (LS) regression and phylogenetic independent contrasts (PIC) to determine what morphological variables were associated with increases in tooth spacing, and 3) used to reconstruct the evolution of feeding related traits within a phylogenetic context. The PCA analysis revealed that within arctoid carnivores, the greatest differences in morphospace were associated with pierce‐feeding, and the early‐diverging seal Enaliarctos was placed within the pinniped morphospace. Increased tooth spacing within Pinnipedia is a result of decreased postcanine crown size. When the evolution of dental characters is reconstructed, ‘enaliarctines’ were found to represent an intermediate stage in evolution between ‘fissiped’ and pinniped carnivores. They retained the limited tooth spacing of terrestrial carnivores, possessed postcanine crown lengths intermediate in size between pinnipeds and fissipeds, and possessed reduced heterodonty characteristic of crown pinnipeds. Our study indicated that pierce‐feeding evolved early within pinnipeds. This suggested either that pierce‐feeding evolved prior to the loss of mastication, or that pierce‐feeding evolved at the same time as loss of mastication, and well before simplification of the dentition was completed.     

Fossilized ontogenies: the contribution of placoderm ontogeny to our understanding of the evolution of early gnathostomes

Placoderms, representing phylogenetically more inclusive jawed vertebrates and successive sister taxa to crown‐group gnathostomes, are critical to our understanding of character evolution within the crown‐group (chondrichthyans + osteichthyans), including developmental characters. Early ontogenetic stages of placoderms are generally poorly known, although some exceptional faunas preserve both embryonic (e.g. from the Gogo Formation, Western Australia) and post‐embryonic individuals (the Miguasha Formation, Canada; Lode Formation, Latvia; Merriganowry Formation, Gogo Formation, Australia). Information provided by these ontogenies is relevant to questions of placoderm taxonomy and phylogeny, but also to broader questions pertinent to vertebrate evolution as a whole, for example, evolution of bone development, evolution of the axial skeleton and evolution of reproduction.     

Carboniferous Onychophora from Montceau‐les‐Mines,France, and onychophoran terrestrialization

The geological age of the onychophoran crown‐group, and when the group came onto land, have been sources of debate. Although stem‐group Onychophora have been identified from as early as the Cambrian, the sparse record of terrestrial taxa from before the Cretaceous is subject to contradictory interpretations. A Late Carboniferous species from the Mazon Creek biota of the USA, Helenodora inopinata, originally interpreted as a crown‐group onychophoran, has recently been allied to early Cambrian stem‐group taxa. Here we describe a fossil species from the Late Carboniferous Montceau‐les‐Mines Lagerstätte, France, informally referred to as an onychophoran for more than 30 years. The onychophoran affinities of Antennipatus montceauensis gen. nov., sp. nov. are indicated by the form of the trunk plicae and the shape and spacing of their papillae, details of antennal annuli, and the presence of putative slime papillae. The poor preservation of several key systematic characters for extant Onychophora, however, prohibits the precise placement of the Carboniferous fossil in the stem or crown of the two extant families, or the onychophoran stem‐group as a whole. Nevertheless, A. montceauensis is the most compelling candidate to date for a terrestrial Paleozoic onychophoran.     

Latitudinal effects on crown shape evolution

Large variations in crown shape are observed across the globe, from plants with wide and deep crowns to those with leaves clustered at the top. While there have been advances in the large‐scale monitoring of forests, little is known about factors driving variations in crown shape with environmental conditions. Previous theoretical research suggests a gradient in crown shape with latitude, due to the effects of sun angle. Yet, it remains unclear whether such changes are also predicted under competition. Using a size‐structured forest‐growth model that incorporates self‐shading from plants and competitive shading from their neighbors, we investigate how changes in site productivity and sun angle shape crown evolution. We consider evolution in two traits describing the top‐heaviness and width‐to‐height ratio of crowns, shaped by trade‐offs reflecting the costs and benefits of alternative architectures. In top‐heavy trees, most of the leaves are at the top half of the trunk. We show that, contrary to common belief, the angle of sun beams per se has only a weak influence on crown shapes, except at low site productivity. By contrast, reduced site productivity has a strong effect, with trees growing in less productive sites keeping their leaves closer to the ground. The crown width‐to‐height ratio is generally higher at a lower site productivity, but this trait is not strongly influenced by any environmental factor. This theoretical analysis brings into question established beliefs about the effects of latitude on crown shapes. By introducing geometry‐related growth constraints caused by shading from both the surrounding forest and the tree on itself, and costs for constructing and maintaining a three‐dimensional crown, our analysis suggests crown shapes may vary with latitude, mostly via effects on overall site productivity, and less because of the angle of the sun.     

Mosaicism in a new Eocene pufferfish highlights rapid morphological innovation near the origin of crown tetraodontiforms

Tetraodontiformes (pufferfishes and kin) is a taxonomically and structurally diverse, widely‐distributed clade of acanthomorphs, whose members often serve as models for genomics and, increasingly, macroevolutionary studies. Morphologically disparate Palaeogene fossils suggest considerable early experimentation, but these flattened specimens often preserve limited information. We present a three‐dimensionally preserved beaked tetraodontiform from the early Eocene (c. 53 Ma) London Clay Formation, UK. Approximately coeval with the oldest crown tetraodontiforms, ?Ctenoplectus williamsi gen. et sp. nov. presents an unprecedented combination of characters, pairing a fused beak‐like dentition with prominent dorsal‐fin spines that insert atop transversely‐expanded pterygiophores roofing the skull. Bayesian total‐evidence tip‐dating analysis indicates that ?Ctenoplectus represents the sister lineage of Triodontidae and highlights considerable levels of homoplasy in early tetraodontiform evolution. According to our dataset, rates of morphological character evolution were elevated at the origin of crown Tetraodontiformes, especially within gymnodonts, but declined after the principal body plans were established. Such ‘early burst’ patterns are regarded as a hallmark of adaptive radiations, but are typically associated with diversification at smaller spatiotemporal scales. However, denser sampling of Neogene and Recent taxa is needed to confirm this pattern.     

Evolutionary analyses of ABC transporters of Dictyostelium discoideum

The ABC superfamily of genes is one of the largest in the genomes of both bacteria and eukaryotes. The proteins encoded by these genes all carry a characteristic 200- to 250-amino-acid ATP-binding cassette that gives them their family name. In bacteria they are mostly involved in nutrient import, while in eukaryotes many are involved in export. Seven different families have been defined in eukaryotes based on sequence homology, domain topology, and function. While only 6 ABC genes in Dictyostelium discoideum have been studied in detail previously, sequences from the well-advanced Dictyostelium genome project have allowed us to recognize 68 members of this superfamily. They have been classified and compared to animal, plant, and fungal orthologs in order to gain some insight into the evolution of this superfamily. It appears that many of the genes inferred to have been present in the ancestor of the crown organisms duplicated extensively in some but not all phyla, while others were lost in one lineage or the other.     

The evolution of jumping in frogs: Morphological evidence for the basal anuran locomotor condition and the radiation of locomotor systems in crown group anurans

Our understanding of the evolution of frog locomotion follows from the work of Emerson in which anurans are proposed to possess one of three different iliosacral configurations: 1) a lateral‐bending system found in walking and hopping frogs; 2) a fore‐aft sliding mechanism found in several locomotor modes; and 3) a sagittal‐hinge‐type pelvis posited to be related to long‐distance jumping performance. The most basal living (Ascaphus) and fossil (Prosalirus) frogs are described as sagittal‐hinge pelvic types, and it has been proposed that long‐distance jumping with a sagittal‐hinge pelvis arose early in frog evolution. We revisited osteological traits of the pelvic region to conduct a phylogenetic analysis of the relationships between pelvic systems and locomotor modes in frogs. Using two of Emerson's diagnostic traits from the sacrum and ilium and two new traits from the urostyle, we resampled the taxa originally studied by Emerson and key paleotaxa and conducted an analysis of ancestral‐character state evolution in relation to locomotor mode. We present a new pattern for the evolution of pelvic systems and locomotor modes in frogs. Character analysis shows that the lateral‐bender, walker/hopper condition is both basal and generally conserved across the Anura. Long‐distance jumping frogs do not appear until well within the Neobatrachia. The sagittal‐hinge morphology is correlated with long‐distance jumping in terrestrial frogs; however, it evolved convergently multiple times in crown group anurans with the same four pelvic traits described herein. Arboreal jumping has appeared in multiple crown lineages as well, but with divergent patterns of evolution involving each of the three pelvic types. The fore‐aft slider morph appears independently in three different locomotor modes and, thus, is a more complex system than previously thought. Finally, it appears that the advent of a bicondylar sacro‐urostylic articulation was originally related to providing axial rigidity to lateral‐bending behaviors rather than sagittal bending. J. Morphol., 2011. © 2010 Wiley‐Liss, Inc.     

Mitochondrial complementation: a possible neglected factor behind early eukaryotic sex

Sex is ancestral in eukaryotes. Meiotic sex differs from bacterial ways of exchanging genetic material by involving the fusion of two cells. We examine the hypothesis that fusion evolved in early eukaryotes because it was directly beneficial, rather than a passive side effect of meiotic sex. We assume that the uptake of (proto)mitochondria into eukaryotes preceded the evolution of cell fusion and that Muller's ratchet operating within symbiont lineages led to the accumulation of lineage‐specific sets of mutations in asexual host cells. We examine whether cell fusion, and the consequent biparental inheritance of symbionts, helps to mitigate the effects of this mutational meltdown of mitochondria. In our model, host cell fitness improves when two independently evolved mitochondrial strains co‐inhabit a single cytoplasm, mirroring mitochondrial complementation found in modern eukaryotes. If fusion incurs no cost, we find that an allele coding for fusion can invade a population of nonfusers. If fusion is costly, there are two thresholds. The first describes a maximal fusing rate (probability of fusion per round of cell division) that is able to fix. An allele that codes for a rate above this threshold can reach a polymorphic equilibrium with nonfusers, as long as the rate is below the second threshold, above which the fusion allele is counter‐selected. Whenever it evolves, fusion increases the population‐wide level of heteroplasmy, which allows mitochondrial complementation and increases population fitness. We conclude that beneficial interactions between mitochondria are a potential factor that selected for cell fusion in early eukaryotes.     

Implications of the new eukaryotic systematics for parasitologists

An accurate understanding of evolutionary relationships is central in biology. For parasitologists, understanding the relationships among eukaryotic organisms allows the prediction of virulence mechanisms, reconstruction of metabolic pathways, identification of potential drug targets, elucidation of parasite-specific cellular processes and understanding of interactions with the host or vector. Here we consider the impact of major recent revisions of eukaryotic systematics and taxonomy on parasitology. The previous, ladder-like model placed some protists as early diverging, with the remaining eukaryotes “progressing” towards a “crown radiation” of animals, plants, Fungi and some additional protistan lineages. This model has been robustly disproven. The new model is based on vastly increased amounts of molecular sequence data, integration with morphological information and the rigorous application of phylogenetic methods to those data. It now divides eukaryotes into six major supergroups; the relationships between those groups and the order of branching remain unknown. This new eukaryotic phylogeny emphasizes that organisms including Giardia, Trypanosoma and Trichomonas are not primitive, but instead highly evolved and specialised for their specific environments. The wealth of newly available comparative genomic data has also allowed the reconstruction of ancient suites of characteristics and mapping of character evolution in diverse parasites. For example, the last common eukaryotic ancestor was apparently complex, suggesting that lineage-specific adaptations and secondary losses have been important in the evolution of protistan parasites. Referring to the best evidence-based models for eukaryotic evolution will allow parasitologists to make more accurate and reliable inferences about pathogens that cause significant morbidity and mortality.     

Evolutionary timescale of monocots determined by the fossilized birth‐death model using a large number of fossil records

Although the phylogenetic relationships between monocot orders are sufficiently understood, a timescale of their evolution is needed. Several studies on molecular clock dating are available, but their results have been biased by their calibration schemes. Recently, the fossilized birth‐death model, a type of Bayesian dating method, was proposed, and it does not require prior calibration and allows the use all available fossils. Using this model, we conducted divergence‐time estimations of monocots to explore their evolutionary timeline without calibration bias. This is the first application of this model to seed plants. The dataset contained the matK and rbcL chloroplast genes of 118 monocot genera covering all extant orders. We employed information from 247 monocot fossils, which exceeded previous dating analyses that used a maximum of 12 monocot fossils. The crown group of monocots was dated to approximately the Late Jurassic–Early Cretaceous periods, and most extant monocot orders were estimated to diverge throughout the Early Cretaceous. Our results overlapped with the divergence time of insect lineages, such as beetles and flies, suggesting an association with pollinators in early monocot evolution. In addition, we proposed three new orders based on divergence time: Orchidales separated from Asparagales and Tofieldiales and Arales separated from Aslimatales.     

Deciphering a global network of functionally associated post‐translational modifications

Various post‐translational modifications (PTMs) fine‐tune the functions of almost all eukaryotic proteins, and co‐regulation of different types of PTMs has been shown within and between a number of proteins. Aiming at a more global view of the interplay between PTM types, we collected modifications for 13 frequent PTM types in 8 eukaryotes, compared their speed of evolution and developed a method for measuring PTM co‐evolution within proteins based on the co‐occurrence of sites across eukaryotes. As many sites are still to be discovered, this is a considerable underestimate, yet, assuming that most co‐evolving PTMs are functionally associated, we found that PTM types are vastly interconnected, forming a global network that comprise in human alone >50 000 residues in about 6000 proteins. We predict substantial PTM type interplay in secreted and membrane‐associated proteins and in the context of particular protein domains and short‐linear motifs. The global network of co‐evolving PTM types implies a complex and intertwined post‐translational regulation landscape that is likely to regulate multiple functional states of many if not all eukaryotic proteins.     

Making sense of ‘lower’ and ‘upper’ stem‐group Euarthropoda,with comments on the strict use of the name Arthropoda von Siebold, 1848

The ever‐increasing number of studies that address the origin and evolution of Euarthropoda – whose extant representatives include chelicerates, myriapods, crustaceans and hexapods – are gradually reaching a consensus with regard to the overall phylogenetic relationships of some of the earliest representatives of this phylum. The stem‐lineage of Euarthropoda includes numerous forms that reflect the major morphological transition from a lobopodian‐type to a completely arthrodized body organization. Several methods of classification that aim to reflect such a complex evolutionary history have been proposed as a consequence of this taxonomic diversity. Unfortunately, this has also led to a saturation of nomenclatural schemes, often in conflict with each other, some of which are incompatible with cladistic‐based methodologies. Here, I review the convoluted terminology associated with the classification of stem‐group Euarthropoda, and propose a synapomorphy‐based distinction that allows ‘lower stem‐Euarthropoda’ (e.g. lobopodians, radiodontans) to be separated from ‘upper stem‐Euarthropoda’ (e.g. fuxianhuiids, Cambrian bivalved forms) in terms of the structural organization of the head region and other aspects of overall body architecture. The step‐wise acquisition of morphological features associated with the origins of the crown‐group indicate that the node defining upper stem‐Euarthropoda is phylogenetically stable, and supported by numerous synapomorphic characters; these include the presence of a deutocerebral first appendage pair, multisegmented head region with one or more pairs of post‐ocular differentiated limbs, complete body arthrodization, posterior‐facing mouth associated with the hypostome/labrum complex, and post‐oral biramous arthropodized appendages. The name ‘Deuteropoda’ nov. is proposed for the scion (monophyletic group including the crown‐group and an extension of the stem‐group) that comprises upper stem‐Euarthropoda and Euarthropoda. A brief account of common terminological inaccuracies in recent palaeontological studies evinces the utility of Deuteropoda nov. as a reference point for discussing aspects of early euarthropod phylogeny.     

Phylogeny and classification of the Asteroidea (Echinodermata)

Post-Palaeozoic asteroids share a large number of derived characters of the ambulacral column and the mouth frame, and constitute the crown group of the monophyletic group Asteroidea. This crown group is here called the Neoasteroidea (new subclass). The stem species of the crown group lived in the Permian or early Triassic and so the evolution of the asteroids parallels that of the echinoids. Character distribution within the Neoasteroidea, especially morphology of the skeleton, digestive system, larvae and tube feet, allows subdivision into four orders (Paxillosida, Notomyotida, Valvatida, Forcipulatida). The latter three orders possess the synapomorphy of suckered tube feet and are united as the Surculifera (new superorder); the Paxillosida are their primitive sister group. Palaeozoic asteroids represent the stem group of the class, and may be divided into plesions according to the order of appearance of synapomorphies with the crown group. Classification of Palaeozoic asteroids requires much further study. The appearance of new characters within the crown group asteroids, such as suckered tube feet, implies that these were absent in the stem group. The range of life-habits possible in Palaeozoic asteroids can thus be partly deduced from evidence provided by living asteroids. Palaeozoic asteroids are deduced to have lacked suckered tube feet and were presumably unable to evert the stomach; hence they were precluded from life on hard substrates and extraoral feeding on epifaunal organisms. It is suggested that they lived on soft substrates by deposit feeding, scavenging and predation on small benthos.     

CO2‐metabolism in early tetrapods revisited: inferences from osteological correlates of gills,skin and lung ventilation in the fossil record

One of the most important physiological changes during the conquest of land by vertebrates was the increasing reliance on lung breathing, with the concomitant decrease in importance of gill breathing. The main problem involved here was to cope with the excessive accumulation of CO₂ in the body and to avoid respiratory acidosis. In the past, several often mutually contradicting hypotheses of CO₂‐elimination via skin, lungs and gills in early tetrapods have been proposed, based on theoretical physiological considerations and comparison with extant air‐breathing fishes and amphibians. This study proposes a revised scenario of CO₂‐elimination in early tetrapods based on fossil evidence, that is recently identified osteological correlates of gills, skin structure and mode of lung ventilation. In stem tetrapods of the Devonian and Carboniferous, O₂‐uptake via the lungs by buccal pumping was decoupled from CO₂‐release via internal gills, and the rather gas‐impermeable skin played a minor role in gaseous exchange. The two main lineages of crown‐group tetrapods, the amphibian and amniote lineage, used different strategies of CO₂‐elimination. As in stem tetrapods, O₂‐uptake and CO₂‐release remained always largely decoupled in temnospondyls, which ventilated their lungs via buccal pumping and relied mainly on their internal gills for CO₂‐release. Temnospondyls were not able to reduce their internal gills before their skin became more gas permeable and their body size was reduced, to shift from internal gills to the skin as the major site of CO₂‐elimination, a pattern that is retained in most lissamphibians. In contrast, internal gills were lost very early in stem amniote evolution. This was associated with the evolution of the more effective aspiration pump that allowed the elimination of the bulk of CO₂ via the lungs, leading to a coupled O₂‐uptake and CO₂‐loss in stem amniotes and later in amniotes.     

Reconstructing pectoral appendicular muscle anatomy in fossil fish and tetrapods over the fins‐to‐limbs transition

The question of how tetrapod limbs evolved from fins is one of the great puzzles of evolutionary biology. While palaeontologists, developmental biologists, and geneticists have made great strides in explaining the origin and early evolution of limb skeletal structures, that of the muscles remains largely unknown. The main reason is the lack of consensus about appendicular muscle homology between the closest living relatives of early tetrapods: lobe‐finned fish and crown tetrapods. In the light of a recent study of these homologies, we re‐examined osteological correlates of muscle attachment in the pectoral girdle, humerus, radius, and ulna of early tetrapods and their close relatives. Twenty‐nine extinct and six extant sarcopterygians were included in a meta‐analysis using information from the literature and from original specimens, when possible. We analysed these osteological correlates using parsimony‐based character optimization in order to reconstruct muscle anatomy in ancestral lobe‐finned fish, tetrapodomorph fish, stem tetrapods, and crown tetrapods. Our synthesis revealed that many tetrapod shoulder muscles probably were already present in tetrapodomorph fish, while most of the more‐distal appendicular muscles either arose later from largely undifferentiated dorsal and ventral muscle masses or did not leave clear correlates of attachment in these taxa. Based on this review and meta‐analysis, we postulate a stepwise sequence of specific appendicular muscle acquisitions, splits, and fusions that led from the ancestral sarcopterygian pectoral fin to the ancestral tetrapod forelimb. This sequence largely agrees with previous hypotheses based on palaeontological and comparative work, but it is much more comprehensive in terms of both muscles and taxa. Combined with existing information about the skeletal system, our new synthesis helps to illuminate the genetic, developmental, morphological, functional, and ecological changes that were key components of the fins‐to‐limbs transition.     

The Complete Mitochondrial Genome Sequence of the Hornwort <Emphasis Type="Italic">Megaceros</Emphasis><Emphasis Type="Italic">aenigmaticus</Emphasis> Shows a Mixed Mode of Conservative Yet Dynamic Evolution in Early Land Plant Mitochondrial Genomes

Land plants possess some of the most unusual mitochondrial genomes among eukaryotes. However, in early land plants these genomes resemble those of green and red algae or early eukaryotes. The question of when during land plant evolution the dramatic change in mtDNAs occurred remains unanswered. Here we report the first completely sequenced mitochondrial genome of the hornwort, Megaceros aenigmaticus, a member of the sister group of vascular plants. It is a circular molecule of 184,908 base pairs, with 32 protein genes, 3 rRNA genes, 17 tRNA genes, and 30 group II introns. The genome contains many genes arranged in the same order as in those of a liverwort, a moss, several green and red algae, and Reclinomonas americana, an early-branching eukaryote with the most ancestral form of mtDNA. In particular, the gene order between mtDNAs of the hornwort and Physcomitrella patens (moss) differs by only 8 inversions and translocations. However, the hornwort mtDNA possesses 4 derived features relative to green alga mtDNAs—increased genome size, RNA editing, intron gains, and gene losses—which were all likely acquired during the origin and early evolution of land plants. Overall, this genome and those of other 2 bryophytes show that mitochondrial genomes in early land plants, unlike their seed plant counterparts, exhibit a mixed mode of conservative yet dynamic evolution. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Libo Li and Bin Wang contributed equally to this work.     

Sizing up the genomic footprint of endosymbiosis

A flurry of recent publications have challenged consensus views on the tempo and mode of plastid (chloroplast) evolution in eukaryotes and, more generally, the impact of endosymbiosis in the evolution of the nuclear genome. Endosymbiont‐to‐nucleus gene transfer is an essential component of the transition from endosymbiont to organelle, but the sheer diversity of algal‐derived genes in photosynthetic organisms such as diatoms, as well as the existence of genes of putative plastid ancestry in the nuclear genomes of plastid‐lacking eukaryotes such as ciliates and choanoflagellates, defy simple explanation. Collectively, these papers underscore the power of comparative genomics and, at the same time, reveal how little we know with certainty about the earliest stages of the evolution of photosynthetic eukaryotes. Editor's suggested further reading in BioEssays Early steps in plastid evolution: current ideas and controversies Abstract Dinoflagellate mitochondrial genomes: stretching the rules of molecular biology Abstract     

Horizontal gene transfer in eukaryotes: The weak‐link model

The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes.