The oldest records of photosynthesis

There is diverse, yet controversial fossil evidence for the existence of photosynthesis 3500 million years ago. Among the most persuasive evidence is the stromatolites described from low grade metasedimentary rocks in Western Australia and South Africa. Based on the understanding of the paleobiology of stromatolites and using pertinent fossil and Recent analogs, these Early Archean stromatolites suggest that phototrophs evolved by 3500 million years ago. The evidence allows further interpretation that cyanobacteria were involved. Besides stromatolites, microbial and chemical fossils are also known from the same rock units. Some microfossils morphologically resemble cyanobacteria and thus complement the adduced cyanobacterial involvement in stromatolite construction. If cyanobacteria had evolved by 3500 million years ago, this would indicate that nearly all prokaryotic phyla had already evolved and that prokaryotes diversified rapidly on the early Earth.     

Geological constraints on detecting the earliest life on Earth: a perspective from the Early Archaean (older than 3.7 Gyr) of southwest Greenland

At greater than 3.7 Gyr, Earth's oldest known supracrustal rocks, comprised dominantly of mafic igneous with less common sedimentary units including banded iron formation (BIF), are exposed in southwest Greenland. Regionally, they were intruded by younger tonalites, and then both were intensely dynamothermally metamorphosed to granulite facies (the highest pressures and temperatures generally encountered in the Earth's crust during metamorphism) in the Archaean and subsequently at lower grades until about 1500 Myr ago. Claims for the first preserved life on Earth have been based on the occurrence of greater than 3.8 Gyr isotopically light C occurring as graphite inclusions within apatite crystals from a 5 m thick purported BIF on the island of Akilia. Detailed geologic mapping and observations there indicate that the banding, first claimed to be depositional, is clearly deformational in origin. Furthermore, the mineralogy of the supposed BIF, being dominated by pyroxene, amphibole and quartz, is unlike well-known BIF from the Isua Greenstone Belt (IGB), but resembles enclosing mafic and ultramafic igneous rocks modified by metasomatism and repeated metamorphic recrystallization. This scenario parsimoniously links the geology, whole-rock geochemistry, 2.7 Gyr single crystal zircon ages in the unit, an approximately 1500 Myr age for apatites that lack any graphite, non-MIF sulphur isotopes in the unit and an inconclusive Fe isotope signature. Although both putative body fossils and carbon-12 enriched isotopes in graphite described at Isua are better explained by abiotic processes, more fruitful targets for examining the earliest stages in the emergence of life remain within greater than 3.7 Gyr IGB, which preserves BIF and other rocks that unambiguously formed at Earth's surface.     

Calibrating the molecular clock: estimates of ground squirrel divergence made using fossil and geological time markers

According to 5-Myr-old fossil evidence, ground squirrels within the genus Spermophilus had diverged into subgenera Spermophilus and Otospermophilus by late Miocene times. Radiometric dating has also provided a precise time for the sudden onset of a geological event, occurring 0.725 Myr ago, that initiated the complete and permanent reproductive isolation of two subspecies within the subgenus Otospermophilus. Since these two subspecies (S. beecheyi beecheyi and S. b. douglasii) readily hybridize with each other under laboratory conditions, allopatric subspeciation is unlikely to have occurred prior to 0.725 Myr ago. We employed Nei's model for estimating genetic distance in units which are linear in time, calibrated on the 0.725-Myr- ago date for initiation of S. b. subspeciation, to test its ability to generate a time scale for subgeneric divergence in keeping with the minimum estimate provided by the fossil record. This represents the most valid test to date of the utility of Nei's model for estimating genetic distance in units which are linear in time. Nei's model was found to underestimate this minimum time by 1 Myr, but it approximated this date after correcting values of D for variation in rates of evolution among loci.      

Origin of the endemic fern genus Diellia coincides with the renewal of Hawaiian terrestrial life in the Miocene

The enigmatic fern genus Diellia, endemic to the Hawaiian archipelago, consists of five extant and one recently extinct species. Diellia is morphologically highly variable, and a unique combination of characters has led to several contrasting hypotheses regarding the relationship of Diellia to other ferns. A phylogenetic analysis of four chloroplast loci places Diellia within 'black-stemmed' rock spleenworts of the species-rich genus Asplenium, as previously suggested by W. H. Wagner. Using an external calibration point, we estimate the divergence of the Diellia lineage from its nearest relatives to have occurred at ca. 24.3 Myr ago matching an independent estimate for the renewal of Hawaiian terrestrial life (ca. 23 Myr ago). We therefore suggest that the ancestor of the Diellia lineage may have been among the first successful colonists of the newly emerging islands in the archipelago. Disparity between morphological and nucleotide sequence variation within Diellia is consistent with a recent rapid radiation. Our estimated time of the Diellia radiation (ca. 2 Myr ago) is younger than the oldest island of Kaua'i (ca. 5.1 Myr ago) but older than the younger major islands of Maui (ca. 1.3 Myr ago), Lana'i (ca. 1.3 Myr ago) and Hawaii (ca. 0.43 Myr ago).     

Isolation from the horse genome of a new DNA transposonbelonging to the Tigger family

Tigger elements are human DNA transposons homologous to the pogo element of Drosophila melanogaster. They contain an open reading frame for a transposase very similar to the major mammalian centromere protein CENP-B. We found in the horse genome a DNA element (Ecatig3) sharing 88% homology with human Tigger3. The presence of Tigger elements in the horse genome confirms previous data that date these elements before the divergence between Perissodactyla and Primates (80–90 Myr ago). Copy number evaluation indicates that the horse element is much more abundant than its human counterpart. Southern blot analysis demonstrates that Ecatig3 elements are extremely homogeneous; this may indicate that the evolution of this DNA transposon has been driven by some kind of selection and has not been neutral.The nucleotide sequence data reported in this paper have been submitted to GenBank and have been assigned the accession number AY382599.     

Oldest coelacanth, from the Early Devonian of Australia

Coelacanths are well-known sarcopterygian (lobe-finned) fishes, which together with lungfishes are the closest extant relatives of land vertebrates (tetrapods). Coelacanths have both living representatives and a rich fossil record, but lack fossils older than the late Middle Devonian (385-390 Myr ago), conflicting with current phylogenies implying coelacanths diverged from other sarcopterygians in the earliest Devonian (410-415 Myr ago). Here, we report the discovery of a new coelacanth from the Early Devonian of Australia (407-409 Myr ago), which fills in the approximately 20 Myr 'ghost range' between previous coelacanth records and the predicted origin of the group. This taxon is based on a single lower jaw bone, the dentary, which is deep and short in form and possesses a dentary sensory pore, otherwise seen in Carboniferous and younger taxa.     

Age of the oldest rocks with biogenic components

In a previous review article [1] it was concluded that it seems that stromatolite-bearing rocks were being produced at 3450–3300 Myr ago (e.g. in Western Australia and Southern Africa), and that Archaean (i.e. >2500 Myr) microfossils showing cell division were in existence by 3200–3000 Myr ago. Furthermore, the evidence for biogenic markers (e.g. putative microfossils, carbon isotopes) in the 3800 Myr-old metamorphosed sedimentary rocks from Isua, West Greenland was regarded as equivocal, although the depositional palaeoenvironment, as deduced from the nature of the Isua rocks, was probably not inimical to earliest life. After due evaluation of all the evidence available in the early 1980's, the review concluded by estimating an age of 4000±100 Myr for the origin of life.In the past 12 years or so, the crude time-scale summarised above has not changed drastically, but new evidence from rock dating, from evaluation of biogenicity, and from the dating of early lunar (and, therefore, terrestrial) impacts, has further narrowed the constraints for the timing of earliest evolution. This new evidence is briefly summarised here. An estimate of 3800±50 Myr is suggested as a plausible time range for the origin of life and the beginning of continuous, unbroken evolution.     

DNA hybridization evidence of hominoid phylogeny: Results from an expanded data set

Summary The living hominoids are human, the two species of chimpanzees, gorilla, orangutan, and nine species of gibbons. The cercopithecoids (Old World monkeys) are the sister group of the hominoids. A consensus about the phylogeny of the hominoids has been reached for the branching order of the gibbons (earliest) and the orangutan (next earliest), but the branching order among gorilla, chimpanzees, and human remains in contention. In 1984 we presented DNA-DNA hybridization data, based on 183 DNA hybrids, that we interpreted as evidence that the branching order, from oldest to most recent, was gibbons, orangutan, gorilla, chimpanzees, and human. In the present paper we report on an expanded data set totaling 514 DNA hybrids, which supports the branching order given above. The ranges for the datings of divergence nodes are Old World monkeys, 25–34 million years (Myr) ago; gibbons, 16.4–23 Myr ago; orangutan, 12.2–17 Myr ago; gorilla, 7.7–11 Myr ago; chimpanzees-human, 5.5–7.7 Myr ago. The possible effects of differences in age at first breeding are discussed, and some speculations about average genomic rates of evolution are presented.     

Palaeobotanical studies from tropical Africa: relevance to the evolution of forest, woodland and savannah biomes

Fossil plants provide data on climate, community composition and structure, all of which are relevant to the definition and recognition of biomes. Macrofossils reflect local vegetation, whereas pollen assemblages sample a larger area. The earliest solid evidence for angiosperm tropical rainforest in Africa is based primarily on Late Eocene to Late Oligocene (ca. 39-26 Myr ago) pollen assemblages from Cameroon, which are rich in forest families. Plant macrofossil assemblages from elsewhere in interior Africa for this time interval are rare, but new work at Chilga in the northwestern Ethiopian Highlands documents forest communities at 28 Myr ago. Initial results indicate botanical affinities with lowland West African forest. The earliest known woodland community in tropical Africa is dated at 46 Myr ago in northern Tanzania, as documented by leaves and fruits from lake deposits. The community around the lake was dominated by caesalpinioid legumes, but included Acacia, for which this, to my knowledge, is the earliest record. This community is structurally similar to modern miombo, although it is different at the generic level. The grass-dominated savannah biome began to expand in the Middle Miocene (16 Myr ago), and became widespread in the Late Miocene (ca. 8 Myr ago), as documented by pollen and carbon isotopes from both West and East Africa.     

Geographic distribution of suitable hosts explains the evolution of specialized gentes in the European cuckoo Cuculus canorus

Background

We recently discovered two composite long terminal repeat (LTR)-retrotransposon-like elements which we named DA (~300 kb) and Xiao (~30 kb), meaning big and small in Chinese respectively. Xiao and DA (three types of DA identified) were found to have been derived from several donor sites and have spread to 30 loci in the human genome, totaling to 5 Mb. Our bioinformatics analyses with the released human, chimp, rhesus macaque, orangutan, and marmoset genomic sequences indicate that DA and Xiao emerged ~25 million years (Myr) ago.

Results

To better understand the evolution of these two complex elements, we investigated various internal junctions of DA and Xiao as well as orthologous genomic sites of the 30 DA/Xiao loci in non-human primates including great apes, lesser apes, Old World monkeys, New World monkeys, and a prosimian. We found that Xiao and type I DA first emerged in the genome between 25 and 18 Myr ago, whereas type II and Type III DAs emerged between 14 and 7 Myr ago. Xiao and DA were most active in great apes, with their amplification peaking during 25-14 and 14-7 Myr ago, respectively. Neither DA nor Xiao seem to have been active in the human and chimp genomes during last 6 Myr.

Conclusion

The study has led to a more accurate age determination of the DA and Xiao elements than our previous bioinformatics analyses, and indicates that the amplification activity of the elements coincided with that of group I HERV-Es during evolution. It has also illustrated an evolutionary path with stepwise structural changes for the elements during past 25 Myr, and in doing so has shed more light on these two intriguing and complex elements that have reshaped our genome.     

Cell evolution and Earth history: stasis and revolution

This synthesis has three main parts. The first discusses the overall tree of life and nature of the last common ancestor (cenancestor). I emphasize key steps in cellular evolution important for ordering and timing the major evolutionary innovations in the history of the biosphere, explaining especially the origins of the eukaryote cell and of bacterial flagella and cell envelope novelties. Second, I map the tree onto the fossil record and discuss dates of key events and their biogeochemical impact. Finally, I present a broad synthesis, discussing evidence for a three-phase history of life. The first phase began perhaps ca 3.5 Gyr ago, when the origin of cells and anoxic photosynthesis generated the arguably most primitive prokaryote phylum, Chlorobacteria (= Chloroflexi), the first negibacteria with cells bounded by two acyl ester phospholipid membranes. After this 'chlorobacterial age' of benthic anaerobic evolution protected from UV radiation by mineral grains, two momentous quantum evolutionary episodes of cellular innovation and microbial radiation dramatically transformed the Earth's surface: the glycobacterial revolution initiated an oxygenic 'age of cyanobacteria' and, as the ozone layer grew, the rise of plankton; immensely later, probably as recently as ca 0.9 Gyr ago, the neomuran revolution ushered in the 'age of eukaryotes', Archaebacteria (arguably the youngest bacterial phylum), and morphological complexity. Diversification of glycobacteria ca 2.8 Gyr ago, predominantly inhabiting stratified benthic mats, I suggest caused serial depletion of 13C by ribulose 1,5-bis-phosphate caboxylase/oxygenase (Rubisco) to yield ultralight late Archaean organic carbon formerly attributed to methanogenesis plus methanotrophy. The late origin of archaebacterial methanogenesis ca 720 Myr ago perhaps triggered snowball Earth episodes by slight global warming increasing weathering and reducing CO2 levels, to yield runaway cooling; the origin of anaerobic methane oxidation ca 570 Myr ago reduced methane flux at source, stabilizing Phanerozoic climates. I argue that the major cellular innovations exhibit a pattern of quantum evolution followed by very rapid radiation and then substantial stasis, as described by Simpson. They yielded organisms that are a mosaic of extremely conservative and radically novel features, as characterized by De Beer's phrase 'mosaic evolution'. Evolution is not evenly paced and there are no real molecular clocks.     

Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics

Mitochondrial DNA sequences are often used to construct molecular phylogenetic trees among closely related animals. In order to examine the usefulness of mtDNA sequences for deep-branch phylogenetics, genes in previously reported mtDNA sequences were analyzed among several animals that diverged 20–600 million years ago. Unambiguous alignment was achieved for stem-forming regions of mitochondrial tRNA genes by virtue of their conservative secondary structures. Sequences derived from stem parts of the mitochondrial tRNA genes appeared to accumulate much variation linearly for a long period of time: nearly 100 Myr for transition differences and more than 350 Myr for transversion differences. This characteristic could be attributed, in part, to the structural variability of mitochondrial tRNAs, which have fewer restrictions on their tertiary structure than do nonmitochondrial tRNAs. The tRNA sequence data served to reconstruct a well-established phylogeny of the animals with 100% bootstrap probabilities by both maximum parsimony and neighbor joining methods. By contrast, mitochondrial protein genes coding for cytochrome b and cytochrome oxidase subunit I did not reconstruct the established phylogeny or did so only weakly, although a variety of fractions of the protein gene sequences were subjected to tree-building. This discouraging phylogenetic performance of mitochondrial protein genes, especially with respect to branches originating over 300 Myr ago, was not simply due to high randomness in the data. It may have been due to the relative susceptibility of the protein genes to natural selection as compared with the stem parts of mitochondrial tRNA genes. On the basis of these results, it is proposed that mitochondrial tRNA genes may be useful in resolving deep branches in animal phylogenies with divergences that occurred some hundreds of Myr ago. For this purpose, we designed a set of primers with which mtDNA fragments encompassing clustered tRNA genes were successfully amplified from various vertebrates by the polymerase chain reaction.Abbreviations AA stem amino acid-acceptor stem - AC stem anticodon stem - COI cytochrome oxidase subunit I - cytb cytochrome b - D stem dihydrouridine stem - MP maximum parsimony - mtDNA mitochondrial DNA - Myr million years - NJ neighbor joining - PCR polymerase chain reaction - Ti transition - T stem tC stem - Tv transversion Correspondence to: Y. Kumazawa     

Miocene skinks and geckos reveal long-term conservatism of New Zealand's lizard fauna

The New Zealand (NZ) lizard fossil record is currently limited to late Quaternary remains of modern taxa. The St Bathans Fauna (early Miocene, southern South Island) extends this record to 19–16 million years ago (Myr ago). Skull and postcranial elements are similar to extant Oligosoma (Lygosominae) skinks and Hoplodactylus (Diplodactylinae) geckos. There is no evidence of other squamate groups. These fossils, along with coeval sphenodontines, demonstrate a long conservative history for the NZ lepidosaurian fauna, provide new molecular clock calibrations and contradict inferences of a very recent (less than 8 Myr ago) arrival of skinks in NZ.     

Extended phylogeny of Aquilegia: the biogeographical and ecological patterns of two simultaneous but contrasting radiations

Studies of the North American columbines (Aquilegia, Ranunculaceae) have supported the view that adaptive radiations in animal-pollinated plants proceed through pollinator specialisation and floral differentiation. However, although the diversity of pollinators and floral morphology is much lower in Europe and Asia than in North America, the number of columbine species is similar in the three continents. This supports the hypothesis that habitat and pollinator specialisation have contributed differently to the radiation of columbines in different continents. To establish the basic background to test this hypothesis, we expanded the molecular phylogeny of the genus to include a representative set of species from each continent. Our results suggest that the diversity of the genus is the result of two independent events of radiation, one involving Asiatic and North American species and the other involving Asiatic and European species. The ancestors of both lineages probably occupied the mountains of south-central Siberia. North American and European columbines are monophyletic within their respective lineages. The genus originated between 6.18 and 6.57 million years (Myr) ago, with the main pulses of diversification starting around 3 Myr ago both in Europe (1.25–3.96 Myr ago) and North America (1.42–5.01 Myr ago). The type of habitat occupied shifted more often in the Euroasiatic lineage, while pollination vectors shifted more often in the Asiatic-North American lineage. Moreover, while allopatric speciation predominated in the European lineage, sympatric speciation acted in the North American one. In conclusion, the radiation of columbines in Europe and North America involved similar rates of diversification and took place simultaneously and independently. However, the ecological drivers of radiation were different: geographic isolation and shifts in habitat use were more important in Europe while reproductive isolation linked to shifts in pollinator specialisation additionally acted in North America.     

New dinosaurs link southern landmasses in the Mid-Cretaceous

Abelisauroid predators have been recorded almost exclusively from South America, India and Madagascar, a distribution thought to document persistent land connections exclusive of Africa. Here, we report fossils from three stratigraphic levels in the Cretaceous of Niger that provide definitive evidence that abelisauroid dinosaurs and their immediate antecedents were also present on Africa. The fossils include an immediate abelisauroid antecedent of Early Cretaceous age (ca. 130-110 Myr ago), early members of the two abelisauroid subgroups (Noasauridae, Abelisauridae) of Mid-Cretaceous age (ca. 110 Myr ago) and a hornless abelisaurid skull of early Late Cretaceous age (ca. 95 Myr ago). Together, these fossils fill in the early history of the abelisauroid radiation and provide key evidence for continued faunal exchange among Gondwanan landmasses until the end of the Early Cretaceous (ca. 100 Myr ago).     

Molecular phylogeny and biogeography of the Korean woodroaches Cryptocercus spp

Phylogenetic relationships and biogeography of Northeast Asian Cryptocercus were inferred based on the DNA sequences of mitochondrial COII and 16S rRNA genes and nuclear 18S rRNA gene. The results suggest that two clades exist in Korean populations. The southwestern population (Cryptocercus from Jiri-san) was more closely related to the populations from Northeast China and eastern Russia than to all the other Korean Cryptocercus. According to molecular-based estimated divergence times, the divergence event occurred between Cryptocercus in Jiri-san, Northeast China and eastern Russia and those in the remaining South Korea during the Miocene (7.5-17.4Myr ago), and then the divergence event between Cryptocercus in Jiri-san and those in Northeast China and eastern Russia occurred 0.8-1.9Myr ago. In the Korean Peninsula, Jiri-san is located in the most southwestern region among the high mountains surveyed. The location is the farthest from Northeast China and eastern Russia among sampling localities in South Korea. Thus, it was unexpected that the southwestern populations are more closely related to those from Northeast China and eastern Russia rather than to the other Korean Cryptocercus. Based on Korean topography and estimated divergence times, possible scenarios are proposed for the current geographical distribution of Korean Cryptocercus.     

The role of immigrants in the assembly of the South American rainforest tree flora

The Amazon lowland rainforest flora is conventionally viewed as comprising lineages that evolved in biogeographic isolation after the split of west Gondwana (ca. 100 Myr ago). Recent molecular phylogenies, however, identify immigrant lineages that arrived in South America during its period of oceanic isolation (ca. 100-3 Myr ago). Long-distance sweepstakes dispersal across oceans played an important and possibly predominant role. Stepping-stone migration from Africa and North America through hypothesized Late Cretaceous and Tertiary island chains may have facilitated immigration. An analysis of inventory plot data suggests that immigrant lineages comprise ca. 20% of both the species and individuals of an Amazon tree community in Ecuador. This is more than an order of magnitude higher than previous estimates. We also present data on the community-level similarity between South American and palaeotropical rainforests, and suggest that most taxonomic similarity derives from trans-oceanic dispersal, rather than a shared Gondwanan history.     

Gene conversions in the horse alpha-globin gene complex

The sequences of the linked alpha 2- and alpha 1-globin genes of the equine BI and BII haplotypes are greater than 99% identical within a 1.2-kb region extending from approximately 75 bp upstream of the putative cap site to a point approximately 150 bp 3' to the poly A addition signal. Differences between the alpha 2 and alpha 1 genes that are common to both haplotypes indicate that a major gene conversion occurred approximately 12 Myr ago and that this has been followed by shorter, more localized, conversions. Interhaplotype (allelic) comparisons at the alpha loci suggest that the BI and BII haplotypes have probably existed independently greater than or equal to 0.5 Myr and that the alpha 1 genes may have undergone a recent interchromosomal gene conversion.      

Origin of tropical American burrowing reptiles by transatlantic rafting

Populations of terrestrial or freshwater taxa that are separated by oceans can be explained by either oceanic dispersal or fragmentation of a previously contiguous land mass. Amphisbaenians, the worm lizards (approx. 165 species), are small squamate reptiles that are uniquely adapted to a burrowing lifestyle and inhabit Africa, South America, Caribbean Islands, North America, Europe and the Middle East. All but a few species are limbless and they rarely leave their subterranean burrows. Given their peculiar habits, the distribution of amphisbaenians has been assumed to be primarily the result of two land-mass fragmentation events: the split of the supercontinent Pangaea starting 200 Myr ago, separating species on the northern land mass (Laurasia) from those on the southern land mass (Gondwana), and the split of South America from Africa 100 Myr ago. Here we show with molecular evidence that oceanic dispersal-on floating islands-played a more prominent role, and that amphisbaenians crossed the Atlantic Ocean in the Eocene (40 Myr ago) resulting in a tropical American radiation representing one-half of all known amphisbaenian species. Until now, only four or five transatlantic dispersal events were known in terrestrial vertebrates. Significantly, this is the first such dispersal event to involve a group that burrows, an unexpected lifestyle for an oceanic disperser.     

Radiation of the Australian flora: what can comparisons of molecular phylogenies across multiple taxa tell us about the evolution of diversity in present-day communities?

The Australian fossil record shows that from ca. 25 Myr ago, the aseasonal-wet biome (rainforest and wet heath) gave way to the unique Australian sclerophyll biomes dominated by eucalypts, acacias and casuarinas. This transition coincided with tectonic isolation of Australia, leading to cooler, drier, more seasonal climates. From 3 Myr ago, aridification caused rapid opening of the central Australian arid zone. Molecular phylogenies with dated nodes have provided new perspectives on how these events could have affected the evolution of the Australian flora. During the Mid-Cenozoic (25-10 Myr ago) period of climatic change, there were rapid radiations in sclerophyll taxa, such as Banksia, eucalypts, pea-flowered legumes and Allocasuarina. At the same time, taxa restricted to the aseasonal-wet biome (Nothofagus, Podocarpaceae and Araucariaceae) did not radiate or were depleted by extinction. During the Pliocene aridification, two Eremean biome taxa (Lepidium and Chenopodiaceae) radiated rapidly after dispersing into Australia from overseas. It is clear that the biomes have different histories. Lineages in the aseasonal-wet biome are species poor, with sister taxa that are species rich, either outside Australia or in the sclerophyll biomes. In conjunction with the fossil record, this indicates depletion of the Australian aseasonal-wet biome from the Mid-Cenozoic. In the sclerophyll biomes, there have been multiple exchanges between the southwest and southeast, rather than single large endemic radiations after a vicariance event. There is need for rigorous molecular phylogenetic studies so that additional questions can be addressed, such as how interactions between biomes may have driven the speciation process during radiations. New studies should include the hitherto neglected monsoonal tropics.