Paleobiological Perspectives on Early Eukaryotic Evolution

Eukaryotic organisms radiated in Proterozoic oceans with oxygenated surface waters, but, commonly, anoxia at depth. Exceptionally preserved fossils of red algae favor crown group emergence more than 1200 million years ago, but older (up to 1600–1800 million years) microfossils could record stem group eukaryotes. Major eukaryotic diversification ∼800 million years ago is documented by the increase in the taxonomic richness of complex, organic-walled microfossils, including simple coenocytic and multicellular forms, as well as widespread tests comparable to those of extant testate amoebae and simple foraminiferans and diverse scales comparable to organic and siliceous scales formed today by protists in several clades. Mid-Neoproterozoic establishment or expansion of eukaryophagy provides a possible mechanism for accelerating eukaryotic diversification long after the origin of the domain. Protists continued to diversify along with animals in the more pervasively oxygenated oceans of the Phanerozoic Eon.Eukaryotic organisms have a long evolutionary history, recorded, in part, by conventional and molecular fossils. For the Phanerozoic Eon (the past 542 million years), eukaryotic evolution is richly documented by the skeletons (and, occasionally, nonskeletal remains) of animals, as well as the leaves, stems, roots, and reproductive organs of land plants. Phylogenetic logic, however, tells us that eukaryotes must have a deeper history, one that began long before the first plant and animal fossils formed. To what extent does the geological record preserve aspects of deep eukaryotic history, and can the chemistry of ancient sedimentary rocks elucidate the environmental conditions under which the eukaryotic cell took shape?     

The terrestrial biota prior to the origin of land plants (embryophytes): a review of the evidence

It is often assumed that life originated and diversified in the oceans prior to colonizing the land. However, environmental constraints in chemical evolution models point towards critical steps leading to the origin of life as having occurred in subaerial settings. The earliest fossil record does not include finds from terrestrial deposits, so much of our understanding about the presence of a terrestrial microbial cover prior to the Proterozoic is based on inference and geochemical proxies that indicate biospheric carbon cycling during the Archaean. Our assessment is that by 2.7 Ga, microbial ecosystems in terrestrial settings were driven by oxygen‐generating, photosynthetic cyanobacteria. Studies of modern organisms indicate that both the origin and primary diversification of the eukaryotes could have occurred in terrestrial settings, shortly after 2.0 Ga, but there is no direct fossil evidence of terrestrial eukaryotes until about 1.1 Ga. At this time, it appears that the diversity of life in non‐marine habitats exceeded that found in marine settings where sulphidic seas may have impaired eukaryotic physiology and retarded evolution. Geochemical proxies indicate the establishment of an extensive soil‐forming microbial cover by 850 Ma, and it is possible that a rise in atmospheric oxygen at this time was due to the evolutionary expansion of green algae into terrestrial habitats. Direct fossil evidence of the earliest terrestrial biotas in the Phanerozoic consists of problematical palynomorphs from the Cambro‐Ordovician of Laurentia. These indicate that the evolution of the first land plants (embryophytes) during the Middle Ordovician took place within a landscape that included aeroterrestrial algae which were actively adapting to selection in subaerial settings.     

Origin and evolution of the grazing guild in new world terrestrial mammals

Although vertebrate herbivory has existed on land for about 300 million years, the grazingadaptation, principally developed in mammals, did not appear until the middle Cenozoic about 30 million years ago. Paleontological evidence indicates that grazing mammals diversified at the time of the spread of grasslands. Recently revised fossil calibrations reveal that the grazing mammal guild originated during the early Miocene in South America about 10-15 million years earlier than it did during the late Miocene in the northern hemisphere. Carbon isotopic analyses of extinct grazers' teeth reveal that this guild originated predominantly in C(3) terrestrial ecosystems. The present-day distribution of C(3) and C(4) grasslands evolved on the global ecological landscape since the late Miocene, after about 7 million years ago.     

The fossil record and biogeography of the Ciehlidae (Actinopterygii: Labroidei)

The family Ciehlidae is a large group of tropical fishes in the order Perciformes, with an estimated number of living species exceeding 1400. The modern distribution of the family Ciehlidae is predominantly in fresh waters of Central and South America, Africa, Madagascar, India and the Middle East, with fossil members known from Africa, Saudi Arabia, the Levant, Europe, South America and Haiti. Many authors have referred to the distribution as being Gondwanan and have postulated that cichlids originated over 130 million years ago, in the Early Cretaceous. However, the suggested evidence for an Early Cretaceous origin of cichlids is equally or more compatible with a much younger age of origin. Based on the biology and distribution of modern and fossil cichlids, it is more probable that they arose less than 65 million years ago, in the Early Tertiary, and crossed marine waters to attain their current distribution.     

The Size of Cells and Organisms in Relation to the Evolution of Embryophytes

Abstract: The earliest O₂-_-evolvers were marine cyanobacteria (3.5 billion years ago) with marine eukaryotic phototrophs from 2.0 billion years ago. These organisms were, and are, poikilo-hydric, i.e., cannot remain hydrated when exposed to a desiccating atmosphere (as can occur for intertidal benthic algae and cy anobacteria at low tide). The smallest marine primarily poikilo-hydric O₂-_-evolvers are close to the lower size limit imposed by non-scaleable components such as minimum genome size and constant membrane thickness, with cyanobacterial unicells 0.65 μn in diameter and eukaryotic unicells 0.95 μm in diameter. The largest (multicellular) marine primarily aquatic poikilohydric O₂-_-evolvers are brown algae at least 60 m long and over 100 kg fresh mass; there are no obvious constraints on the max imum size of such organisms. In freshwaters the size range for primarily poikilohydric O₂-_-evolving organisms is smaller, due to the absence of very large organisms. An even smaller size range characterizes terrestrial algae and cyanobacteria which have occurred for about 1 billion years. Desiccation-tolerant cyanobacterium and algae (intertidal, freshwater, terrestrial) are at the lower end of the size ranges. Embryophytic terrestrial O₂-_-evolvers arose some 450 million years ago and were than all poikilohydric and (probably) desiccation-tolerant. Embryophytic defining structural features re quire organisms of at least 100 μm equivalent spherical diameter for both gametophyte and sporophyte phases. Primarily poi kilohydric embryophytes are not more than 1 m tall as a result of a mechanistically mysterious size limit for desiccation-tolerant organisms. Homoiohydric embryophytes evolved some 420 mil lion years ago in the sporophyte phase (later to become the dominant terrestrial vegetation) and possibly in the gameto phyte phase (although no such homoiohydric gametophytes are known today). The homoiohydric features of gas spaces, stomata, cuticle, endohydric water conducting system and water and nutrient uptake structures require an organism at least 5 mm high; this has implications for the minimum size of mega-spores and seeds. The tallest homoiohydric plants are (or were within historic times) 130 m high, with height constrained by re source costs of the synthesis and maintenance of the mechanical and water conduction systems, andbr of xylem water trans port. Secondarily poikilohydric embryophytes in aquatic, or very damp terrestrial, habitats are derived from homoiohydric plants; they retain most homoiohydric features but are not functionally homoiohydric. The smaller secondarily poikilohydric plants are less than one tenth of the size of the smallest functionally homoiohydric plants.     

The origin of metazoan development: a palaeobiological perspective

The rapid diversification of early Metazoa remains one of the most puzzling events in the fossil record. Several models have been proposed to explain a critical aspect of this event: the origin of Metazoan development. These include the origin of the eukaryotic cell, environmental triggers, key innovations or selection among cell lineages. Here, the first three hypotheses are evaulated within a phylogenetic framework using fossil, molecular and developmental evidence. Many elements of metazoan development are widely distributed among unicellular eukaryotes, yet only 3 of the 23 multicellular eukaryotic lineages evolved complex development. Molecular evidence indicates the lineage leading to the eukaryotic cell is nearly as old as the eubacterial and archaebacterial lineages, although the symbiotic events established that the eukaryotic cell probably occurred about 1.5 billion years ago. Yet Metazoa did not appear until 1000 to 600 million years ago (Myr), suggesting the origin of metazoan development must be linked to either an environmental trigger, perhaps an increase in atmospheric oxygen, or key innovations such as the development of collagen. Yet the first model fails to explain the unique appearance of complex development in Metazoa, while the latter fails to explain the simultaneous diversification of several ‘protist’ groups along with the Metazoa. A more complete model of the origin of metazoan development combines environmental triggering of a series of innovations, with successive innovations generating radiations of metazoan clades as lineages breached functional thresholds. The elaboration of new cell classes and the appearance of such developmental innovations as cell sheets may have been of particular importance. Evolutionary biologists often implicitly assume that evolution is a uniformitarian, time-homogeneous process without strong temporal asymmetries in evolutionary mechanisms, rate or context. Yet evolutionary patterns do exhibit such asymmetries, raising the possibility that such innovations as metazoan development impose non-uniformities of evolutionary process.     

Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi

In the past, molecular clocks have been used to estimate divergence times among animal phyla, but those time estimates have varied widely (1200-670 million years ago, Ma). In order to obtain time estimates that are more robust, we have analysed a larger number of genes for divergences among three well-represented animal phyla, and among plants, animals and fungi. The time estimate for the chordate-arthropod divergence, using 50 genes, is 993 +/- 46 Ma. Nematodes were found to have diverged from the lineage leading to arthropods and chordates at 1177 +/- 79 Ma. Phylogenetic analyses also show that a basal position of nematodes has strong support (p > 99%) and is not the result of rate biases. The three-way split (relationships unresolved) of plants, animals and fungi was estimated at 1576 +/- 88 Ma. By inference, the basal animal phyla (Porifera, Cnidaria, Ctenophora) diverged between about 1200-1500 Ma. This suggests that at least six animal phyla originated deep in the Precambrian, more than 400 million years earlier than their first appearance in the fossil record.     

Fire-adapted traits of Pinus arose in the fiery Cretaceous

? The mapping of functional traits onto chronograms is an emerging approach for the identification of how agents of natural selection have shaped the evolution of organisms. Recent research has reported fire-dependent traits appearing among flowering plants from 60 million yr ago (Ma). Although there are many records of fossil charcoal in the Cretaceous (65-145 Ma), evidence of fire-dependent traits evolving in that period is lacking. ? We link the evolutionary trajectories for five fire-adapted traits in Pinaceae with paleoatmospheric conditions over the last 250 million yr to determine the time at which fire originated as a selective force in trait evolution among seed plants. ? Fire-protective thick bark originated in Pinus c. 126 Ma in association with low-intensity surface fires. More intense crown fires emerged c. 89 Ma coincident with thicker bark and branch shedding, or serotiny with branch retention as an alternative strategy. These innovations appeared at the same time as the Earth's paleoatmosphere experienced elevated oxygen levels that led to high burn probabilities during the mid-Cretaceous. ? The fiery environments of the Cretaceous strongly influenced trait evolution in Pinus. Our evidence for a strong correlation between the evolution of fire-response strategies and changes in fire regime 90-125 Ma greatly backdates the key role that fire has played in the evolution of seed plants.     

Bees diversified in the age of eudicots

Reliable estimates on the ages of the major bee clades are needed to further understand the evolutionary history of bees and their close association with flowering plants. Divergence times have been estimated for a few groups of bees, but no study has yet provided estimates for all major bee lineages. To date the origin of bees and their major clades, we first perform a phylogenetic analysis of bees including representatives from every extant family, subfamily and almost all tribes, using sequence data from seven genes. We then use this phylogeny to place 14 time calibration points based on information from the fossil record for an uncorrelated relaxed clock divergence time analysis taking into account uncertainties in phylogenetic relationships and the fossil record. We explore the effect of placing a hard upper age bound near the root of the tree and the effect of different topologies on our divergence time estimates. We estimate that crown bees originated approximately 123 Ma (million years ago) (113–132 Ma), concurrently with the origin or diversification of the eudicots, a group comprising 75 per cent of angiosperm species. All of the major bee clades are estimated to have originated during the Middle to Late Cretaceous, which is when angiosperms became the dominant group of land plants.     

Similarities in eukaryotic genomes

1. The degree of overlap between the human genome and that of other eukaryotes is considered. Biochemical and molecular studies have shown that all eukaryotic organisms evolved from a common progenator that lived several billion years ago. 2. From a geneological point of view, all eukaryotes are related and their genes are all descended from common ancestors. 3. However, most of the DNA in eukaryotic genomes is not transcribed and has been free to drift in nucleotide sequence. Therefore, the question of overlap can only be applied meaningfully to the few per cent of the genome that is expressed. 4. During the last billion years many genes have duplicated and diverged and new genes have been formed by accretion of domains copied from other genes (exon shuffling). 5. The rate of genetic divergence has been such that only a few portions coding for pieces of highly conserved proteins are still shared by all eukaryotes including those that diverged over 600 million years ago. 6. On the other hand, a fairly large number of shared genes can be recognized among species that separated within the last few hundred million years. 7. Human genes have a high degree of identity with homologs in closely related organisms such as other mammals and a decreasing level of identity with their homologs in more distantly related species.     

A molecular timeline for the origin of photosynthetic eukaryotes

The appearance of photosynthetic eukaryotes (algae and plants) dramatically altered the Earth's ecosystem, making possible all vertebrate life on land, including humans. Dating algal origin is, however, frustrated by a meager fossil record. We generated a plastid multi-gene phylogeny with Bayesian inference and then used maximum likelihood molecular clock methods to estimate algal divergence times. The plastid tree was used as a surrogate for algal host evolution because of recent phylogenetic evidence supporting the vertical ancestry of the plastid in the red, green, and glaucophyte algae. Nodes in the plastid tree were constrained with six reliable fossil dates and a maximum age of 3,500 MYA based on the earliest known eubacterial fossil. Our analyses support an ancient (late Paleoproterozoic) origin of photosynthetic eukaryotes with the primary endosymbiosis that gave rise to the first alga having occurred after the split of the Plantae (i.e., red, green, and glaucophyte algae plus land plants) from the opisthokonts sometime before 1,558 MYA. The split of the red and green algae is calculated to have occurred about 1,500 MYA, and the putative single red algal secondary endosymbiosis that gave rise to the plastid in the cryptophyte, haptophyte, and stramenopile algae (chromists) occurred about 1,300 MYA. These dates, which are consistent with fossil evidence for putative marine algae (i.e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution.     

Evolutionary dynamics of vertebrate body mass range

Change in body mass with time has been considered for many clades, often with reference to Cope's rule, which predicts a tendency to increase in body size. A more general rule, namely increase in the range of body mass with time, is analyzed here for vertebrates. The log range of log vertebrate body mass is shown to increase linearly and highly significantly with the log of duration of clade existence. The resulting regression equations are used to predict the origin age, initial body mass, and subsequent dynamics of body mass range for primate clades such as the New World monkeys (Platyrrhini, 32 million years ago, initial mass of 1.7 kg) and the Anthropoidea (57 million years ago, initial mass of 0.12 kg), tested against the primate fossil record. Using these methods, other major primate clades such as Lemuriformes and Adapoidea are also estimated to have originated in the Tertiary (63 and 64 million years ago, respectively), with only the Plesiadapiformes originating in the Cretaceous (83 million years ago). Similarities of body mass range between primate and other vertebrate sister groups are discussed. Linear relationships of log range and log duration are considered with respect to Brownian processes, with the expected regression coefficients from the latter explored through simulations. The observed data produce regression coefficients that overlap with or are higher than those under Brownian processes. Overall, the analyses suggest the dynamics of vertebrate body mass range in morphologically disparate clades are highly predictable over many tens of million years and that the dynamics of phenotypic characteristics can assist molecular clock and fossil models in dating evolutionary events.     

Seaweeds in cold seas: evolution and carbon acquisition

Much evidence suggests that life originated in hydrothermal habitats, and for much of the time since the origin of cyanobacteria (at least 2.5 Ga ago) and of eukaryotic algae (at least 2.1 Ga ago) the average sea surface and land surface temperatures were higher than they are today. However, there have been at least four significant glacial episodes prior to the Pleistocene glaciations. Two of these (approx. 2.1 and 0.7 Ga ago) may have involved a 'Snowball Earth' with a very great impact on the algae (sensu lato) of the time (cyanobacteria, Chlorophyta and Rhodophyta) and especially those that were adapted to warm habitats. By contrast, it is possible that heterokont, dinophyte and haptophyte phototrophs only evolved after the Carboniferous-Permian ice age (approx. 250 Ma ago) and so did not encounter low (相似文献   

Evolution of photoprotection mechanisms upon land colonization: evidence of PSBS‐dependent NPQ in late Streptophyte algae

Light is the energy source for photosynthetic organisms but, if absorbed in excess, it can drive to the formation of reactive oxygen species and photoinhibition. One major mechanism to avoid oxidative damage in plants and algae is the dissipation of excess excitation energy as heat, called non‐photochemical quenching (NPQ). Eukaryotic algae and plants, however, rely on two different proteins for NPQ activation, the former mainly depending on LHCSR (Lhc‐like protein Stress Related; previously called Li818, Light Induced protein 818), whereas in the latter the major role is played by a distinct protein, PSBS (photosystem II subunit S). In the moss Physcomitrella patens, which diverged from vascular plants early after land colonization, both these proteins were found to be present and active in inducing NPQ, suggesting that during plants evolution both mechanisms co‐existed. In order to investigate in more detail NPQ adaptation toward land colonization, we analyzed Streptophyte algae, the latest organisms to diverge from the land plants ancestors. Among them we found evidence of a PSBS‐dependent NPQ in species belonging to Charales, Coleochaetales and Zygnematales, the latest groups to diverge from land plants ancestors. On the contrary earlier diverging algae, as Mesostigmatales and Klebsormidiales, likely rely on LHCSR for their NPQ activation. Presented evidence thus suggests that PSBS‐dependent NPQ, although possibly present in some Chlorophyta, was stably acquired in the Cambrian period about 500 million years ago, before late Streptophyte algae diverged from plants ancestors.     

Geological evidence of oxygenic photosynthesis and the biotic response to the 2400-2200 Ma “Great Oxidation Event”

Fossil evidence of photosynthesis, documented in the geological record by microbially laminated stromatolites, microscopic fossils, and carbon isotopic data consistent with the presence of Rubisco-mediated CO₂-fixation, extends to ～3500 million years ago. Such evidence, however, does not resolve the time of origin of oxygenic photosynthesis from its anoxygenic photosynthetic evolutionary precursor. Though it is evident that cyanobacteria, the earliest-evolved O₂-producing photoautotrophs, existed before ～2450 million years ago — the onset of the “Great Oxidation Event” (GOE) that forever altered Earth’s environment — O₂-producing photosynthesis seems certain to have originated hundreds of millions of years earlier. How did Earth’s biota respond to the GOE? Four lines of evidence are here suggested to reflect this major environmental transition: (1) rRNA phylogeny-correlated metabolic and biosynthetic pathways document evolution from an anaerobic (pre-GOE) to a dominantly oxygen-requiring (post-GOE) biosphere; (2) consistent with the rRNA phylogeny of cyanobacteria, their fossil record evidences the immediately post-GOE presence of cyanobacterial nostocaceans characterized by specialized cells that protect their oxygen-labile nitrogenase enzyme system; (3) the earliest known fossil eukaryotes, obligately aerobic phytoplankton and putative algae, closely post-date the GOE; and (4) microbial sulfuretums are earliest known from rocks deposited during and immediately after the GOE, their apparent proliferation evidently spurred by an increase of environmental oxygen and a resulting upsurge of metabolically useable sulfate and nitrate. Though the biotic response to the GOE is a question new to paleobiology that is yet largely unexplored, additional evidence of its impact seems certain to be uncovered.     

Carbon isotopes support the presence of extensive land floras pre-dating the origin of vascular plants

Multiple lines of evidence indicate that Earth's land masses became green some 2.7 Ga ago, about 1 billion years after the advent of life. About 2.2 billion years later, land plants abruptly appear in the fossil record and diversify marking the onset of ecologically complex terrestrial communities that persist to the present day. Given this long history of land colonization, surprisingly few studies report direct fossil evidence of emergent vegetation prior to the continuous record of life on land that starts in the mid-Silurian (ca. 420–425 Ma ago). Here we compare stable carbon isotope signatures of fossils from seven Ordovician–Silurian (450–420 Ma old) Appalachian biotas with signatures of coeval marine organic matter and with stable carbon isotope values predicted for Ordovician and Silurian liverworts (BRYOCARB model). The comparisons support a terrestrial origin for fossils in six of the biotas analyzed, and indicate that some of the fossils represent bryophyte-grade plants. Our results demonstrate that extensive land floras pre-dated the advent of vascular plants by at least 25 Ma. The Appalachian fossils represent the oldest direct evidence of widespread colonization of continents. These findings provide a new search image for macrofossil assemblages that contain the earliest stages of land plant evolution. We anticipate they will fuel renewed efforts to search for direct fossil evidence to track the origin of land plants and eukaryotic life on continents further back in geologic time.     

Origin of land plants: Do conjugating green algae hold the key?

Background  

The terrestrial habitat was colonized by the ancestors of modern land plants about 500 to 470 million years ago. Today it is widely accepted that land plants (embryophytes) evolved from streptophyte algae, also referred to as charophycean algae. The streptophyte algae are a paraphyletic group of green algae, ranging from unicellular flagellates to morphologically complex forms such as the stoneworts (Charales). For a better understanding of the evolution of land plants, it is of prime importance to identify the streptophyte algae that are the sister-group to the embryophytes. The Charales, the Coleochaetales or more recently the Zygnematales have been considered to be the sister group of the embryophytes However, despite many years of phylogenetic studies, this question has not been resolved and remains controversial.     

The evolution and diversification of Dicers in plants

Most multicellular organisms regulate developmental transitions by microRNAs, which are generated by an enzyme, Dicer. Insects and fungi have two Dicer-like genes, and many animals have only one, yet the plant, Arabidopsis, has four. Examining the poplar and rice genomes revealed that they contain five and six Dicer-like genes, respectively. Analysis of these genes suggests that plants require a basic set of four Dicer types which were present before the divergence of mono- and dicotyledonous plants ( approximately 200 million years ago), but after the divergence of plants from green algae. A fifth type of Dicer seems to have evolved in monocots.     

A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution

The African clawed frogs (Silurana and Xenopus), model organisms for scientific inquiry, are unusual in that allopolyploidization has occurred on multiple occasions, giving rise to tetraploid, octoploid, and dodecaploid species. To better understand their evolution, here we estimate a mitochondrial DNA phylogeny from all described and some undescribed species. We examine the timing and location of diversification, and test hypotheses concerning the frequency of polyploid speciation and taxonomy. Using a relaxed molecular clock, we estimate that extant clawed frog lineages originated well after the breakup of Gondwana, about 63.7 million years ago, with a 95% confidence interval from 50.4 to 81.3 million years ago. Silurana and two major lineages of Xenopus have overlapping distributions in sub-Saharan Africa, and dispersal-vicariance analysis suggests that clawed frogs originated in central and/or eastern equatorial Africa. Most or all extant species originated before the Pleistocene; recent rainforest refugia probably acted as "lifeboats" that preserved existing species, rather than "species pumps" where many new successful lineages originated. We estimate that polyploidization occurred at least six times in clawed frogs.     

Did some red alga‐derived plastids evolve via kleptoplastidy? A hypothesis

The evolution of plastids has a complex and still unresolved history. These organelles originated from a cyanobacterium via primary endosymbiosis, resulting in three eukaryotic lineages: glaucophytes, red algae, and green plants. The red and green algal plastids then spread via eukaryote–eukaryote endosymbioses, known as secondary and tertiary symbioses, to numerous heterotrophic protist lineages. The number of these horizontal plastid transfers, especially in the case of red alga‐derived plastids, remains controversial. Some authors argue that the number of plastid origins should be minimal due to perceived difficulties in the transformation of a eukaryotic algal endosymbiont into a multimembrane plastid, but increasingly the available data contradict this argument. I suggest that obstacles in solving this dilemma result from the acceptance of a single evolutionary scenario for the endosymbiont‐to‐plastid transformation formulated by Cavalier‐Smith & Lee (1985). Herein I discuss data that challenge this evolutionary scenario. Moreover, I propose a new model for the origin of multimembrane plastids belonging to the red lineage and apply it to the dinoflagellate peridinin plastid. The new model has several general and practical implications, such as the requirement for a new definition of cell organelles and in the construction of chimeric organisms.