A molecular-clock date for the origin of the animal phyla

Although the reliability of the molecular clock for determining divergence times that are not visible in the fossil record has been questioned, the amino-acid sequence differences in the α and β haemoglobins of a variety of living vertebrates do not support this view. While the molecular clock is clearly probabilistic rather than metronomic, it can be shown that the α and β haemoglobins have been evolving at a statistically equal rate since they first appeared some 450–500 million years ago. If this rate has always been constant for all globins, then the percentage sequence differences between several invertebrate and some vertebrate globins can be used to indicate that the initial radiation of the animal phyla occurred at least 900–1000 million years ago. ?Molecular evolution, Metazoa, haemoglobin.     

The origin of animal phyla and the new phylum Procoelomata

BergstrÖm, Jan 1989 07 15: The origin of animal phyla and the new phylum Procoelomata. Lethaia , Vol. 22, pp. 259–269. Oslo. ISSN 0024–1164.
A model of metazoan evolution presented previously (BergstrÖm 1986 in Zoologica Scripta 15 ) explains deuterostomian characters as derived from protostomian ones through loosening of the constraints in the spiralian type of morphogenesis. This fits phylogenies derived from studies of molecular sequences. The model helps explain (1) the well-known mixture of proto- and deuterostomian features in several groups; (2) the difficulties in making a phylogeny based on comparative anatomy, and (3) the fossil explosion in the Cambrian. Since protostomian features such as a ciliated locomotory sole and a pelagic larva with ciliary bands are widely distributed in branches of the phylogenetic tree, they must have been present in the stem of the tree. Most probably the stem forms were pseudosegmented, which helps explain how segmentation, oligomery and non-segmentation could evolve repeatedly in derived groups. Origination of new phyla involved macroevolutionary changes primarily in the mode of feeding and locomotion. The stem phylum, from which most other phyla appear to have been derived directly, is here named the Procoelomata. Machaeridian-type animals are referred to it. The Ediacaran-type Precambrian fossils Cannot be placed in the metazoan evolutionary tree. * Biochemical evolution, Cambrian fossil explosion, Deuterostomia, eukaryote evolution, Machaeridia. macroevolution, Precambrian fossils. Procoelomata, Protostomia .     

Divergence estimates and early evolutionary history of Figitidae (Hymenoptera: Cynipoidea)

We examine the phylogenetic relationships of Figitidae and discuss host use within this group in light of our own and previously published divergence time data. Our results suggest Figitidae, as currently defined, is not monophyletic. Furthermore, Mikeiinae and Pycnostigminae are sister‐groups, nested adjacent to Thrasorinae, Plectocynipinae and Euceroptrinae. The recovery of Pycnostigminae as sister‐group to Mikeiinae suggests two major patterns of evolution: (i) early Figitidae lineages demonstrate a Gondawanan origin (Plectocynipinae: Neotropical; Mikeiinae and Thrasorinae: Australia; Pycnostigminae: Africa); and (ii) based on host records for Mikeiinae, Thrasorinae and Plectocynipinae, Pycnostigminae are predicted to be parasitic on gall‐inducing Hymenoptera. The phylogenetic position of Parnips (Parnipinae) was unstable, and various analyses were conducted to determine the impact of this uncertainty on both the recovery of other clades and inferred divergence times; when Parnips was excluded from the total evidence analysis, Cynipidae was found to be sister‐group to [Euceroptrinae + (Plectocynipinae (Thrasorinae + (Mikeiinae + Pycnostigminae)))], with low support. Divergence dating analyses using BEAST indicate the stem‐group node of Figitidae to be c. 126 Ma; the dipteran parasitoids (Eucoilinae and Figitinae), were estimated to have a median age of 80 and 88 Ma, respectively; the neuropteran parasitoids (Anacharitinae), were estimated to have a median age of 97 Ma; sternorrhynchan hyperparasitoids (Charipinae), were estimated to have a median age of 110 Ma; the Hymenoptera‐parasitic subfamilies (Euceroptinae, Plectocynipinae, Trasorinae, Mikeiinae, Pycnostigminae, and Parnipinae), ranged in median ages from 48 to 108 Ma. Rapid radiation of Eucoilinae subclades appears chronologically synchronized with the origin of their hosts, Schizophora (Diptera). Overall, the exclusion of Parnips from the BEAST analysis did not result in significant changes to divergence estimates. Finally, though sparsely represented in the analysis, our data suggest Cynipidae have a median age of 54 Ma, which is somewhat older than the age of Quercus spp (30–50 Ma), their most common host.     

Chromosomal sex-determining regions in animals, plants and fungi

The independent evolution of sex chromosomes in many eukaryotic species raises questions about the evolutionary forces that drive their formation. Recent advances in our understanding of these genomic structures in mammals in parallel with alternate models such as the monotremes, fish, dioecious plants, and fungi support the idea of a remarkable convergence in structure to form large, non-recombining regions with discrete evolutionary strata. The discovery that evolutionary events similar to those that have transpired in humans have also occurred during the formation of sex chromosomes in organisms as divergent as the plant Silene, the fungus Cryptococcus and the fish medaka highlights the importance of future studies in these systems. Such investigation will broaden our knowledge of the evolution and plasticity of these ubiquitous genomic features underlying sexual dimorphism and reproduction.     

The tubulins of animals,plants, fungi and protists implications for metazoan evolution

Summary -Tubulin subunits from trout (S. gairdneri) sperm tails, sea urchin (S. purpuratus) cilia, protistan alga (C. elongatum) flagella and rose (Paul's Scarlet) cytoplasm have been characterized by limited proteolytic cleavage with the enzymeStaphylococcus aureus protease and electrophoresis of the digestion products on SDS-PAGE. The resulting patterns corresponded to either of two major types representative of animal and non-animal -tubulins, respectively. A total of 28 -tubulins have now been characterized by this method. They are classified in this paper according to the type of cleavage pattern generated by the enzymeS. aureus protease. The implications of these results for metazoan evolution are discussed.     

Not plants or animals: a brief history of the origin of Kingdoms Protozoa, Protista and Protoctista.

In the wake of Darwin's evolutionary ideas, mid-nineteenth century naturalists realized the shortcomings of the long established two-kingdom system of organismal classification. Placement in a natural scheme of Protozoa, Protophyta, Phytozoa and Bacteria, microorganisms that exhibited plant-like and animal-like characteristics but obviously differed in organization from larger plants and animals, challenged traditional classification. The attempts of naturalists to classify these organisms outside the constraints of the plant and animal kingdoms led to concepts of additional kingdoms (Protozoa, Protista, Protoctista, etc.) to accommodate the nature of these organisms as not true plants or animals.     

Conservation of amino acid transporters in fungi, plants and animals

When comparing the transporters of three completely sequenced eukaryotic genomes--Saccharomyces cerevisiae, Arabidopsis thaliana and Homo sapiens--transporter types can be distinguished according to phylogeny, substrate spectrum, transport mechanism and cell specificity. The known amino acid transporters belong to five different superfamilies. Two preferentially Na(+)-coupled transporter superfamilies are not represented in the yeast and Arabidopsis genomes, whereas the other three groups, which often function as H(+)-coupled systems, have members in all investigated genomes. Additional superfamilies exist for organellar transport, including mitochondrial and plastidic carriers. When used in combination with phylogenetic analyses, functional comparison might aid our prediction of physiological functions for related but uncharacterized open reading frames.     

Molecular clocks, molecular phylogenies and the origin of phyla

Erwin, Douglas H. 1989 07 15: Molecular clocks, molecular phylogenies and the origin of phyla. Lethaia , Vol. 22, pp. 251–257. Oslo. ISSN 0024–1164.
Protein, RNA and DNA sequences have been widely used to construct phylogenies and to calculate divergence times using a molecular clock. Reliance on molecular information is particularly attractive when fossil evidence is missing or equivocal, as in the Cambrian metazoan radiation. I consider the applicability of molecular clocks and phylogenetic analysis of molecular data to the origin of metazoan phyla, and conclude that molecular information is often ambiguous or misleading. Amino acid sequences are of limited use because the redundancy of the genetic code masks patterns of descent, while in a nucleotide sequence only four potential states exist at each site (the four nucleotide bases). In each case, homoplasy may often go undetected. The application of a molecular clock to resolve the timing of the metazoan radiation is unwarranted, while molecular phylogenetic reconstruction should be approached with care. A potentially more useful technique for phylogenetic reconstruction would be the use of patterns of genome structure and organization as characters. * Molecular clock, phylogenetics, metazoan radiation, origin of phyla .     

Inheritance and recombination of mitochondrial genomes in plants, fungi and animals

It is generally assumed that mitochondrial genomes are uniparentally transmitted, homoplasmic and nonrecombining. However, these assumptions draw largely from early studies on animal mitochondrial DNA (mtDNA). In this review, we show that plants, animals and fungi are all characterized by episodes of biparental inheritance, recombination among genetically distinct partners, and selfish elements within the mitochondrial genome, but that the extent of these phenomena may vary substantially across taxa. We argue that occasional biparental mitochondrial transmission may allow organisms to achieve the best of both worlds by facilitating mutational clearance but continuing to restrict the spread of selfish genetic elements. We also show that methodological biases and disproportionately allocated study effort are likely to have influenced current estimates of the extent of biparental inheritance, heteroplasmy and recombination in mitochondrial genomes from different taxa. Despite these complications, there do seem to be discernible similarities and differences in transmission dynamics and likelihood of recombination of mtDNA in plant, animal and fungal taxa that should provide an excellent opportunity for comparative investigation of the evolution of mitochondrial genome dynamics.     

In silico prediction of the peroxisomal proteome in fungi,plants and animals

In an attempt to improve our abilities to predict peroxisomal proteins, we have combined machine-learning techniques for analyzing peroxisomal targeting signals (PTS1) with domain-based cross-species comparisons between eight eukaryotic genomes. Our results indicate that this combined approach has a significantly higher specificity than earlier attempts to predict peroxisomal localization, without a loss in sensitivity. This allowed us to predict 430 peroxisomal proteins that almost completely lack a localization annotation. These proteins can be grouped into 29 families covering most of the known steps in all known peroxisomal pathways. In general, plants have the highest number of predicted peroxisomal proteins, and fungi the smallest number.     

The evolution of embryogeny in seed plants and the developmental origin and early history of endosperm

For almost a century, the formation of endosperm from a second and distinctive fertilization event has been viewed as a unique feature of flowering plants. However, until recently, the evolutionary origin of this unique embryo-nourishing entity remained a mystery. Based upon comparative developmental analysis of reproduction among basal angiosperms and their closest extant relatives, the Gnetales (Ephedra, Gnetum, and Welwitschia), it is possible to construct an explicit hypothesis of the events that led to the evolutionary establishment of double fertilization and endosperm. The formulation of this historical record is derived entirely from and dependent upon the determination of reproductive features that are likely to have characterized the common ancestors of angiosperms and Gnetales. Current evidence is most congruent with the concept that a process of double fertilization first evolved in a common ancestor of the Gnetales and angiosperms. Initially, however, the second fertilization product was diploid and yielded a supernumerary embryo. Subsequent to the divergence of the angiosperm lineage from its closest relatives (which include the Gnetales), modification of the development of the supernumerary embryo (derived from the second fertilization event) led to the establishment of an embryo-nourishing endosperm. Comparative analysis of patterns of embryogeny within Gnetales and angiosperms establishes that embryo development in the ancestors of flowering plants (with a rudimentary process of double fertilization) was ab initio cellular, and not free nuclear, as had previously been assumed. Thus, it is likely that the earliest flowering plants displayed an ab initio cellular pattern of endosperm development, whose expression was inherited from that of the supernumerary embryo of the ancestors of flowering plants.     

Divergence time estimates for major cephalopod groups: evidence from multiple genes

This is the first study to use both molecular and fossil data to date the divergence of taxa within the coleoid cephalopods (octopus, squid, cuttlefish). A dataset including sequences from three nuclear and three mitochondrial genes (3415 bp in total) was used to investigate the evolutionary divergences within the group. Divergence time analyses were performed using the Thorne/Kishino method of analysis which allows multiple constraints from the fossil record and permits rates of molecular evolution to vary on different branches of a phylogenetic tree. The data support a Paleozoic origin of the Orders Vampyromorpha, Octopoda and the majority of the extant higher level decapodiform taxa. These estimated divergence times are considerably older than paleontological estimates. The major lineages within the Order Octopoda were estimated to have diverged in the Mesozoic, with a radiation of many taxa around the Cretaceous/Cenozoic boundary. Higher level decapodiform phylogenetic relationships appear to have been obscured due to an ancient diversification of this group. © The Willi Hennig Society 2006.     

Evolution of the mitochondrial genome: protist connections to animals, fungi and plants

The past decade has seen the determination of complete mitochondrial genome sequences from a taxonomically diverse set of organisms. These data have allowed an unprecedented understanding of the evolution of the mitochondrial genome in terms of gene content and order, as well as genome size and structure. In addition, phylogenetic reconstructions based on mitochondrial DNA (mtDNA)-encoded protein sequences have firmly established the identities of protistan relatives of the animal, fungal and plant lineages. Analysis of the mtDNAs of these protists has provided insight into the structure of the mitochondrial genome at the origin of these three, mainly multicellular, eukaryotic groups. Further research into mtDNAs of taxa ancestral and intermediate to currently characterized organisms will help to refine pathways and modes of mtDNA evolution, as well as provide valuable phylogenetic characters to assist in unraveling the deep branching order of all eukaryotes.     

Adaptive response to oxidative stress: Bacteria, fungi, plants and animals

Reactive oxygen species (ROS) are continuously produced and eliminated by living organisms normally maintaining ROS at certain steady-state levels. Under some circumstances, the balance between ROS generation and elimination is disturbed leading to enhanced ROS level called "oxidative stress". The primary goal of this review is to characterize two principal mechanisms of protection against oxidative stress - regulation of membrane permeability and antioxidant potential. The ancillary goals of this work are to describe up to date knowledge on the regulation of the previously mentioned mechanisms and to identify areas of prospective research and emerging directions in investigation of adaptation to oxidative stress. The ubiquity for challenges leading to oxidative stress development calls for identification of common mechanisms. They are cysteine residues and [Fe,S]-clusters of specific regulatory proteins. The latter mechanism is realized via SoxR bacterial protein, whereas the former mechanism is involved in operation of bacterial OxyR regulon, yeast H(2)O(2)-stimulon, plant NPR1/TGA and Rap2.4a systems, and animal Keap1/Nrf2, NF-κB and AP-1, and others. Although hundreds of studies have been carried out in the field with different taxa, the comparative analysis of adaptive response is quite incomplete and therefore, this work aims to cover a plethora of phylogenetic groups to delineate common mechanisms. In addition, this article raises some questions to be elucidated and points out future directions of this research. The comparative approach is used to shed light on fundamental principles and mechanisms of regulation of antioxidant systems. The idea is to provide starting points from which we can develop novel tools and hypothesis to facilitate meaningful investigations in the physiology and biochemistry of organismic response to oxidative stress.     

广义柏科主要分类群起源时间的推测

通过构建分子钟对广义柏科主要分类群的起源时间进行探讨。采用相对速率检验法分析广义柏科mat K、rbc L进化速率的稳定性,结果显示rbc L的非同义替代速率只在Pinaceae与Taxodiaceae的分类群及柏科北半球的支系(Cupressoideae)之间通过相对速率检验,而Pinaceae与柏科南半球分支(Callitrodeae)之间没有通过相对速率检验。mar K基因的非同义替代速率在Pinaceae与广义柏科的所有分类群之间通过相对速率检验。根据通过相对速率检验的分类群之间的遗传距离和基因进化速率,计算它们发生分歧的时间。据此推测,杉科的主要分类群Taiwanioideae、Athrotaxidoideae、Sequoioideae与其他分支发生分歧的时间均在侏罗纪,支持现存杉科在侏罗纪就已经建立起来的观点;Cupressaceae(s．s．)的两个支系(亚科)发生分歧的时间在124Ma之前,相当于早白垩世早期,可能由于南北古大陆的完全分离,其祖先居群被分隔成两个亚群,随后各自演化为不同的支系。Callitirodeae、Cupressoideae各属发生分歧的时间也均在白垩纪,表明Cupressaceae(s．s．)在白垩纪就已经建立起来。     

Phylogenetic detection of numerous gene duplications shared by animals,fungi and plants

Background  

Gene duplication is considered a major driving force for evolution of genetic novelty, thereby facilitating functional divergence and organismal diversity, including the process of speciation. Animals, fungi and plants are major eukaryotic kingdoms and the divergences between them are some of the most significant evolutionary events. Although gene duplications in each lineage have been studied extensively in various contexts, the extent of gene duplication prior to the split of plants and animals/fungi is not clear.     

Closely coupled evolutionary history of ecto‐ and endosymbionts from two distantly related animal phyla

The level of integration between associated partners can range from ectosymbioses to extracellular and intracellular endosymbioses, and this range has been assumed to reflect a continuum from less intimate to evolutionarily highly stable associations. In this study, we examined the specificity and evolutionary history of marine symbioses in a group of closely related sulphur‐oxidizing bacteria, called Candidatus Thiosymbion, that have established ecto‐ and endosymbioses with two distantly related animal phyla, Nematoda and Annelida. Intriguingly, in the ectosymbiotic associations of stilbonematine nematodes, we observed a high degree of congruence between symbiont and host phylogenies, based on their ribosomal RNA (rRNA) genes. In contrast, for the endosymbioses of gutless phallodriline annelids (oligochaetes), we found only a weak congruence between symbiont and host phylogenies, based on analyses of symbiont 16S rRNA genes and six host genetic markers. The much higher degree of congruence between nematodes and their ectosymbionts compared to those of annelids and their endosymbionts was confirmed by cophylogenetic analyses. These revealed 15 significant codivergence events between stilbonematine nematodes and their ectosymbionts, but only one event between gutless phallodrilines and their endosymbionts. Phylogenetic analyses of 16S rRNA gene sequences from 50 Cand. Thiosymbion species revealed seven well‐supported clades that contained both stilbonematine ectosymbionts and phallodriline endosymbionts. This closely coupled evolutionary history of marine ecto‐ and endosymbionts suggests that switches between symbiotic lifestyles and between the two host phyla occurred multiple times during the evolution of the Cand. Thiosymbion clade, and highlights the remarkable flexibility of these symbiotic bacteria.     

The origin and early evolution of plants

Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes – revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).