Dating the Monocot–Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes

We estimated the dates of the monocot–dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset. Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed. Three reliable split events were used as calibration points and for cross references. Both the method based on the assumption of a constant rate and the Li–Tanimura unequal-rate method were used to estimate divergence times. The phylogenetic analyses indicated that nonsynonymous substitution rates of cp genomes are unequal among tracheophyte lineages. For this reason, the constant-rate method gave overestimates of the monocot–dicot divergence and the age of core eudicots, especially when fast-evolving monocots were included in the analysis. In contrast, the Li–Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records. Combining estimates calibrated by two known fossil nodes and the Li–Tanimura method, we propose that monocots branched off from dicots 140–150 Myr ago (late Jurassic–early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100–115 Myr ago (Albian–Aptian of the Cretaceous). These estimates indicate that both the monocot–dicot divergence and the core eudicots age are older than their respective fossil records.     

Should the Teaching of Biological Evolution Include the Origin of Life?

The development of mainstream research on the origin of life as an outcome of Darwinian evolution is discussed. It is argued that prebiotic evolution and the origin of life should not be excluded from the syllabus and should be part of classes on biological evolution, and that the transition from non-living to living matter is best understood when seen as part of evolutionary biology. The wide acceptance of evolutionary approaches to the study of the emergence of life in European and Latin American countries is discussed.     

Long or Heavy? Physiological Constraints in the Evolution of Antlers

The evolution of the investment in exaggerated secondary sexual traits is a topic of great interest for scientists. Despite antlers in the family Cervidae being one of the most interesting allometric structures, the nature of the relationships between antler and body size, and the influence of physiological factors driving the evolution of these characters, still remain unclear. In this paper, I examine these relationships in depth using the largest sample size ever studied (43 species). Under the hypothesis that antler growth may be limited by skeleton size as this process requires the allocation of huge amounts of mineral resources to the antlers, skeleton-related variables may more accurately explain these allometric relationships. The existence of physiological constraints should therefore be more clearly highlighted when studying the relationships between body size variables and the relative investment in the antler (measured as length or mass of antler per kg of skeleton). Results show that antler length is best described as being linearly related to head-body length rather than other measurements of size, and antler weight has a quadratic relationship with body mass. However, the relative investment in antler length (related to skeleton mass) is independent of body size variables, while the relative investment in antler mass has a quadratic relationship with shoulder height. The results obtained for antler mass reflect the existence of physiological constraints in the evolution of antlers, which are greater for larger sized species. On the other hand, the evolution of antler length may be linked to other factors, most probably sociobiological and biomechanical ones.     

The Origin of Life: Chemical Evolution of a Metabolic System in a Mineral Honeycomb?

For the RNA-world hypothesis to be ecologically feasible, selection mechanisms acting on replicator communities need to be invoked and the corresponding scenarios of molecular evolution specified. Complementing our previous models of chemical evolution on mineral surfaces, in which selection was the consequence of the limited mobility of macromolecules attached to the surface, here we offer an alternative realization of prebiotic group-level selection: the physical encapsulation of local replicator communities into the pores of the mineral substrate. Based on cellular automaton simulations we argue that the effect of group selection in a mineral honeycomb could have been efficient enough to keep prebiotic ribozymes of different specificities and replication rates coexistent, and their metabolic cooperation protected from extensive molecular parasitism. We suggest that mutants of the mild parasites persistent in the metabolic system can acquire useful functions such as replicase activity or the production of membrane components, thus opening the way for the evolution of the first autonomous protocells on Earth.     

Causation and the Origin of Life. Metabolism or Replication First?

The conceptual gulf that separates the 'metabolism first' and 'replication first' mechanisms for the emergence of life continues to cloud the origin of life debate. In the present paper we analyze this aspect of the origin of life problem and offer arguments in favor of the 'replication first' school. Utilizing Wicken's two-tier approach to causation we argue that a causal connection between replication and metabolism can only be demonstrated if replication would have preceded metabolism. In conjunction with existing empirical evidence and theoretical reasoning, our analysis concludes that there is no substantive evidence for a 'metabolism first' mechanism for life's emergence, while a coherent case can be made for the 'replication first' group of mechanisms. The analysis reaffirms our conviction that life is an extreme expression of kinetic control, and that the emergence of metabolic pathways can be understood by considering life as a manifestation of 'replicative chemistry'.     

Are monophyly and synapomorphy the same or different? Revisiting the role of morphology in phylogenetics

Species are groups of organisms, marked out by reproductive (replicative) properties. Monophyletic taxa are groups of species, marked out by synapomorphies. In Nelson’s analysis, monophyly and synapomorphy are identical relations. Monophyly and synapomorphy, however, are not equivalent relations. Monophyly is epistemically not accessible, whereas synapomorphy is epistemically accessible through character analysis. Monophyly originates with speciation, the two sister‐species that come into being through the splitting of the ancestral species lineage forming a monophyletic taxon at the lowest level of inclusiveness. Synapomorphy provides the empirical evidence for monophyly, inferred from character analysis in the context of a three‐taxon statement. If synapomorphy and monophyly were equivalent, phylogenetic systematists should find a single tree, instead of multiple equally parsimonious trees. Understanding synapomorphy as the relevant evidence for phylogenetic inference reveals a category mistake in contemporary phylogenetics: the treatment of morphological characters mapped onto molecular trees as synapomorphies and homoplasies. The mapping of morphological characters onto nodes of a molecular tree results in an empirically empty procedure for synapomorphy discovery. Morphological synapomorphies and homoplasies can only be discovered by morphological and combined analyses. The use of morphology in phylogenetic inference in general is defended by examples from Laurales and Squamata in particular. To make empirical evidence scientifically relevant in order to search for concordance, or dis‐concordance, of phylogenetic signal, is certainly more fruitful for phylogenetics than the uncritical mapping of morphological traits on a molecular scaffold. © The Willi Hennig Society 2010.     

The Evolution of the Cenozoic Terrestrial Mammalian Predator Guild in South America: Competition or Replacement?

South America was isolated from other continents during most of the Cenozoic, developing a singular mammalian fauna. In contrast to North America, Europe, Asia, and Africa, up to the late Neogene, the carnivore adaptive zone in South America was populated by crocodiles (Sebecidae), large snakes (Madtsoiidae), large birds (Phorusrhacidae), and metatherian mammals (Sparassodonta). Sparassodonta were varied and comprised a wide range of body masses (≈ 2–50 kg) and food habits. Their diversity decreased towards the late Miocene (Huayquerian Stage/Age) and the group became extinct in the “middle” Pliocene (≈ 3 Ma, Chapadmalalan Stage/Age). Several authors have suggested that the cause of this decline and extinction was the ingression of carnivorans to South America (about 6–7 Ma ago), because they competed with the Sparassodonta; although this hypothesis has been criticized in recent years. With the intention of testing the hypothesis of “competitive displacement,” we review the fossil record of South American Sparassodonta and Carnivora, collect data about diversity, estimate size and diet, and determine first and last appearances. The diversity of Sparassodonta is low relative to that of Carnivora throughout the Cenozoic with the early Miocene (Santacrucian Stage/Age) showing the greatest diversity with 11 species. In the late Miocene-middle Pliocene (Huayquerian Stage/Age), the fossil record shows overlap of groups, and the Sparassodonta’s richness curve begins to decline with the first record of Carnivora. Despite this overlap, carnivorans diversity ranged from four or fewer species in the late Miocene-Pliocene to a peak of around 20 species in the early Pleistocene (Ensenadan Stage/Age). Carnivora was initially represented by small-sized, omnivorous species, with large omnivores first appearing in the Chapadmalalan Stage/Age. Over this period, Sparassodonta was represented by large and small hypercarnivores and a single large omnivorous species. From this review of the fossil record, it is suggested that factors other than competitive displacement may have caused the extinction of the Sparassodonta.     

The Origin and Evolution of Metabolic Pathways: Why and How did Primordial Cells Construct Metabolic Routes?

The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution. In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present on the primordial Earth imposed an important selective pressure, favoring those primordial heterotrophic cells that became able to synthesize those molecules. Thus, the emergence of metabolic pathways allowed primitive organisms to become increasingly less dependent on exogenous sources of organic compounds. Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria, and Eukarya reveal that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the emergence of new metabolic abilities. Among these gene elongations, gene and operon duplications played a crucial role since they can lead to the (immediate) appearance of new genetic material that, in turn, might undergo evolutionary divergence, giving rise to new genes coding for new metabolic abilities. Concerning the mechanisms of pathway assembly, both the analysis of completely sequenced genomes and directed evolution experiments strongly support the patchwork hypothesis, according to which metabolic pathways have been assembled through the recruitment of primitive enzymes that could react with a wide range of chemically related substrates. However, the analysis of the structure and organization of genes belonging to ancient metabolic pathways, such as histidine biosynthesis, suggests that other different hypothesis, i.e., the retrograde hypothesis, may account for the evolution of some steps within metabolic pathways.     

Floral Variation in Tepals,Sterile and Fertile Stamens of Kingdonia uniflora (Ranunculaceae) with Reference to Pollinators and Pollination

To understand the influence of different floral organs of Kingdonia uniflora to the pollinators and pollination, we divided the flowers into four groups, A, with the sterile stamens removed, B, with the tepals removed, C, with the fertile　stamens removed and D, without the remove of any organ. The results showed that the insects visiting frequency were 0.4 time h in group A, 0 time h in group B, 0. 9 time h in group C and 2. 2 time h in group D. The percentage of pollinated flowers was 29.09% in group A, 40. 38% in group B, 70.91% in group C and 91. 67% in group D. The percentage of pollinated carpels was 17.77% in group A, 20.94% in group B, 40.58% in group C and 75.27% in group D respectively. The relationships between the insect visiting frequency and the nectarial secretion of the sterile stamens were observed in the field. To compare with group D, the decrease of the rate of pollinated flower and the carpel was group A > group B>group C. To combine the observation of the relationships between the nectarial secretion of the sterile stamens and the insect visiting frequency, we considered that the sterile stamens with nectar as the reward of the visiting insects play the most important rule for the pollinators and pollination. However, the tepals that could afford the platform of staining and moving of the insects on the flowers are also important for the pollinators. The fertile stamens that could form the chromatic to attract some of the pollinators and supply the pollen grains as the food of some pollinators play less important rule .     

The Origin and Dispersal of the “Lower” Hamamelidae

The “lower” Hamamelidae sensu Endress (1989a) comprises seven families: Trochodendraceae, Tetracentraceae, Cercidiphyllaceae, Myrothamnaceae, Eupteleaceae, Platanaceae and Hamamelidaceae. In the present paper, the systematic position, modern distribution pattern and fossil history of each family are analyzed, and the origin and dispersal of them are discussed according to the principle of the unity between the phylogeny and distribution of plants. The paper consists of three parts. The conclusions are as follows: 1. The center of distribution According to Takhtajan's (1986) regionalization of the world flora, there are 13 distribution types in the “lower” Hamamelidae (Table 1 ). Eastern Asiatic Region, with five families, 19 genera and 73 species, ranks the first based on the numbers of species, genera and families. Four families: Trochodendraceae, Tetracentraceae, Cercidiphyllaceae and Eupteleaceae which were considered as more primitive in the “lower” Hamamelidae and three genera: Disanthus, Exbucklandia and Rhodoleia, primitive in the Hamamelidaceae, are all found in Eastern Asiatic Region. In addition, the groups at different evolutionary stages in the “lower” Hamamelidae survive in this region. Indochinese Region, with two families, 15 genera and 32 species, ranks the second. It was shown that southern Eastern Asiatic region and northern Indochinese Region are the distribution center of the “lower”Hamamelidae based on further analysis (see Table 2). 2. The place and time of the origin The fossil records of the “lower” Hamamelidae are abundant in angiosperms. Nordenskioldia, supposed as the extinct ancestral group of Trochodendraceae and Tetracentraceae, was widely distributed during the latest Cretaceous and the early Tertiary in the Northern Hemisphere; Trochodendroides appeared during the Cretaceous in North America, former USSR and Japan; the ancestral group of Cercidiphyllaceae, the Joffrea-Nyssidum complex, also occurred during the Cretaceous in the middle and higher latitude area of the Norhern Hemisphere. In addition, the earliest fossil records of the Eupteleaceae, Platanaceae and Hamamelidaceae appeared in North America, Europe and Asia of the Northern Hemisphere respectively. Therefore, the Laurasian origin of the “lower” Hamamelidae is supported by fossil evidence. On the other hand, the fossil data are still insufficient to determine the place of the origin, especially because the fossil records are rather poor in Asia. For this reason, the analyses of birthplace should combine with the information from the distribution of the primitive groups or outgroup of the “lower” Hamamelidae. Based on the statistics of distribution types, there are four primitive families in the “lower” Hamamelidae and three primitive genera in the Hamamelidaceae in southern Eastern Asiatic Region and northern Indochinese Region. Platanus kerrii Gagnep. of the Platanaceae, distributed in northern Vietnam, is considered as one of the most primitive species which has survived in modern times in this family because of its pistillate inflorescence comprising 10-12 heads. The Magnoliaceae was selected as an outgroup in our other paper “A phylogenetic analysis of families in the Hamamelidae” (Lu et al. 1991 ). All its 13 genera and most species occur from East to Southeast Asia, but in North America only three genera are found. Takhtajan (1969) considered that it was plants of the Magnoliaceae that were dispersed from East Asia to North America. Because the primitive groups of the “lower” Hamamelidae and its outgroup almost occur in the same area, their ancestor also appeared most probably in this area according to the principle of common origin. It was inferred that the area from southern Eastern Asiatic Region to northern Indochinese Region is the birthplace of the “lower"” Hamamelidae. The differentiation of the “lower” Hamamelidae took place rather early in angiosperms. The origin of them may be traced at least back to the Barremian of the early Cretaceous according to pollen fossil records. From more unequivocal fossil evidence, Platanoid plants appeared during the late Albian of the early Cretaceous, and the Trochodendraceae, Tetracentraceae, Cercidiphyllaceae and Hamamelidaceae diverged from their ancestral groups respectively no later than the late Cretaceous (Fig. 6). 3. The causes for the formation of the modern distribution pattern The “lower” Hamamelidae is a. rather old group. It is one of the most abundant and widespread components of fossil floras in the Northern Hemisphere during the late Cretaceous-middle Tertiary, the interval, when the global temperature was warm, although the extant Trochodendraceae, Tetracentraceae, Cercidiphyllaceae and Eupteleaceae which are now confined to East Asia are monotypical or oligotypical families. This distribution pattern indicates that most plants became extinct in Europe, northern Asia and North America because of the climatic changes during the late Tertiary, and especially the Quaternary glaciation, but East Asia, usually called “plant refuge”during the glacial period, became the survival place of many plants. From the viewpoint of evolution, these four families might be “living fossil plants” preserved from the Tertiary. The distribution of Hamamelidaceae is disjunct, but the causes leading to this pattern are not the same in different genera. The disjunction among Europe, North America, Australia and southern Africa is due to the tectonic movements of the earth; , and that between southeastern Europe-northern West Asia and southeastern Asia is developed as a result of the Quaternary glaciation. Fothergilla found from Carolina to Alabama in the United States and Hamamelis disjunct between East Asia and North America were widely distributed during the Tertiary in the Northern Hemisphere (Hu & Chaney 1940). The formation of their distribution patterns is a synthetic process owing to the tectonic movements and the Quaternary glaciation. Parrotia and Parrotiopsis, endemic to Iran and the West Himalayas respectively, are very similar in morphology. They might have a common ancestor, and the latter is more primitive than the former. It seems that several groups in the Hamamelidaceae were dispersed from east to west in Eurasia. Of the five genera in the Southern Hemisphere, Dicoryphe and Trichocladus are Madagascarian and southern African, and Ostrearia, Neostrearia and Noahdendron occur in northeastern Australia. They are usually considered as rather isolated groups, but Hufford and Endress (1989) found that they are closely related. The African genera might be dispersed from Asia via India, Sri Lanka and Lemuria continent; the Australian Hamamelidaceae also from Asia, but via the islands distributed in the Pacific Ocean. The Myrothamnaceae, comprising 2 species distributed in Madagascar and southern Africa, is closely related to the Hamamelidaceae. Based on morphological analyses, an evolutionary series exists among Myrothamnus, Dicoryphe and Trichocladus in which the distribution patterns are the same, and Myrothamnus is more specialized than the two genera of the Hamamelidaceae. 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Endosymbiotic Origin of Chloroplasts in Plant Cells’ Evolution

Russian Journal of Plant Physiology - The theory of endosymbiotic origin of chloroplasts has become basal in present-day biology. In this regard, the emergence of eukaryotic photosynthesis has been...     

Park or Ride? Evolution of Infant Carrying in Primates

Few mammalian orders carry their infants clinging to the mother's fur. I investigated the evolution of carrying behavior in primates and the life-history and ecological correlates of infant care patterns. Primates are ideal for the study as there is variation in infant care patterns. Primate infants are left hidden in nests or parked in trees, both of which strategies I term parking, and are carried orally or ride clinging to the mother's fur: riding. Infant carrying has evolved several times in the Primates and, once evolved, it has been conserved. Significant energetic costs of riding are indicated as riding species maintain smaller home ranges than those of non-riders of the same body size. With body size and phylogenetic influences taken into account, riders appear to incur a reproductive cost by weaning and breeding later than parkers. Although riders do not have lower birth rates than those of parkers, their later age at first reproduction leads to their having a lower reproductive rate, measured by the intrinsic rate of population increase. Precociality of infants is not correlated with either riding or nesting behavior. Although non-nesting species have larger litter sizes, their infants are not significantly smaller, nor are their neonatal brains relatively smaller. Although riding may have some energetic and reproductive costs, its repeated evolution in the Primates suggests that it also has some benefits, the most likely being a reduced mortality risk for carried infants.     

Are There Laws of Genome Evolution?

Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.     

Cause or effect? The spatial organization of pathogens and the gut microbiota in disease

The human gut hosts a dense and diverse microbial community, spatially organized in multiple scales of structure. Here, we review how microbial organization differs between health and disease. We describe how changes in spatial organization may induce alterations in gut homeostasis, concluding with a future outlook to reveal causality.     

The Soft Underbelly of Evolution?

Evolution and the origin of life are separate, if connected, topics, but they are frequently conflated??especially by creationists. Regarding the natural origin of life as ??the soft underbelly?? of evolution, creationists argue that it is impossible, improbable, or insusceptible to scientific investigation. Underlying their arguments is the hope that the failure of scientific research on the origin of life is evidence for a supernatural account. It is crucial for teachers to understand the nature of science in order to be able to explain why appeals to the supernatural are out of place in explaining the origin of life and why scientific research on the origin of life is not intrinsically a threat to faith.