Biochemical Evolution and the History of Life

1988 ◽  
Vol 1 ◽  
pp. 138-145
Author(s):  
W. Ford Doolittle
Keyword(s):  
Molecular Biology ◽  
Data Base ◽  
Sequence Data ◽  
Darwinian Evolution ◽  
Phylogenetic Distance ◽  
Homologous Proteins ◽  
Random Mutation ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
History Of

Molecular biology has contributed to the construction of the neoDarwinian synthesis, as it is articulated in the 1980's, in two ways. First, it has provided a nearly complete understanding of the processes of DNA replication and expression, and mutation. We know in detail how genotypes are passed on and how random mutation can provide the variation which must be present in populations if natural selection is to “cause” evolution. (We do not yet understand in detail how genotype determines phenotype in any complex multicellular organism, but there is probably no barrier other than complexity in our way.) Second, molecular biology has provided us with a data base from which to draw conclusions about phylogenetic relationships between species, or between genes, and a powerful way of approaching that data base. Zuckerkandl and Pauling's (1965) contention – that comparisons of amino acid or nucleotide sequences of homologous proteins or nucleic acids from contemporary species should allow measurements of phylogenetic distance – has been amply confirmed. Earlier chapters in this volume provide some details about methods and their application to major groups of organisms. Here I would like to discuss what molecular sequence data, and phylogenetic conclusions drawn from them, might have to say about the very earliest stages of Darwinian evolution, before there were cells.

Across Lydekker's Line - first report of mite harvestmen (Opiliones : Cyphophthalmi : Stylocellidae) from New Guinea

2007 ◽  
Vol 21 (3) ◽  
pp. 207 ◽  
Author(s):  
Ronald M. Clouse ◽  
Gonzalo Giribet
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
New Guinea ◽  
Single Male ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
Biogeographic Region ◽  
Molecular Phylogenetic ◽  
History Of

Opiliones (harvestmen) in the suborder Cyphophthalmi are not known to disperse across oceans and each family in the suborder is restricted to a clear biogeographic region. While undertaking a revisionary study of the South-east Asian family Stylocellidae, two collections of stylocellids from New Guinea were noted. This was a surprising find, since the island appears never to have had a land connection with Eurasia, where the rest of the family members are found. Here, 21 New Guinean specimens collected from the westernmost end of the island (Manokwari Province, Indonesia) are described and their relationships to other cyphophthalmids are analysed using molecular sequence data. The specimens represent three species, Stylocellus lydekkeri, sp. nov., S. novaguinea, sp. nov. and undescribed females of a probable third species, which are described and illustrated using scanning electron microscope and stereomicroscope photographs. Stylocellus novaguinea, sp. nov. is described from a single male and it was collected with a juvenile and the three females of the apparent third species. Molecular phylogenetic analyses indicate that the new species are indeed in the family Stylocellidae and they therefore reached western New Guinea by dispersing through Lydekker’s line – the easternmost limit of poor dispersers from Eurasia. The New Guinean species may indicate at least two episodes of oceanic dispersal by Cyphophthalmi, a phenomenon here described for the first time. Alternatively, the presence in New Guinea of poor dispersers from Eurasia may suggest novel hypotheses about the history of the island.

scholarly journals Biogeography and Cophylogeny of Paussus favieri(Carabidae, Paussinae) and Pheidole pallidula(Hymenoptera, Myrmicinae)

2019 ◽  
Vol 2 ◽  
Author(s):  
Davide Bergamaschi ◽  
Wendy Moore ◽  
Andrea Di Giulio
Keyword(s):  
Sequence Data ◽  
Population Level ◽  
Nuclear Markers ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Pheidole Pallidula ◽  
History Of ◽  
Dispersal Events ◽  
European Populations ◽  
Mitochondrial And Nuclear Markers

The myrmecophilous carabid beetle, Paussus favieri, has a circum-Mediterranean distribution and it is completely dependent upon its host ant Pheidole pallidula during all stages of its life history. Using molecular sequence data we inferred the phylogenies of the populations of both the beetle and its ant host to determine if there are signs of co-evolution. A total of 34 P. favieri from France, Spain, Portugal, Morocco and Tunisia and 42 Ph. pallidula workers from the same countries, plus Greece and Italy, were collected and analyzed. Many mitochondrial and nuclear markers were sequenced, but only COI was evolving fast enough to infer the population-level phylogenies of the beetles and the ants. Preliminary analyses suggest that the European populations of P. favieri are derived from a single dispersal event from Africa, while several dispersal events are suggested for Ph. pallidula. We found the topologies of host and parasite trees to be generally congruent, as would be expected if the host and parasite have had a history of co-evolution or co-divergence.

An annotated checklist of the chaetonotidan Gastrotricha from India

Zootaxa ◽  
2021 ◽  
Vol 5027 (3) ◽  
pp. 332-350
Author(s):  
TAPAS CHATTERJEE ◽  
M. ANTONIO TODARO
Keyword(s):  
Sequence Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
History Of Research ◽  
High Incidence ◽  
History Of ◽  
Molecular Sequencing ◽  
Annotated Checklist ◽  
Rule Out

India has a long history of research on freshwater and marine Gastrotricha. In more than 110 years of study on Order Chaetonotida, two families consisting of 11 genera and 39 species have been described. Thirty of these species are taxa originally described from other continents, while only nine species (7 freshwater, 2 marine) are only known from India. The large percentage (77%) of so-called cosmopolitan species in India has contributed to the phenomenon known as the “meiofauna paradox”. However, a careful review of the pertaining literature provides a different biogeographical picture of the chaetonotidan fauna of India. Herein we show that the high incidence of European and North American species reported from India is mainly due to a mixture of misidentification and species lumping. In fact, for only 12 species there are enough data that would make the Indian specimens morphological similar to taxa previously reported from Europe and/or North America. However, without the appropriate molecular sequence data for comparison, there is no way to rule out the possibility of cryptic speciation.We conclude that further sampling throughout India and the use of more powerful microscopical techniques (e.g., DIC optics) and molecular sequencing will reveal more species and improve the quality of re-descriptions of those (9 spp.) that so far appear to be endemic to the subcontinent. Here we recommend six species to be excluded from the fauna of India while another 11 species (non endemic to India) should be considered dubitatively present in the Indian fauna.  

scholarly journals TESTING FOR EVOLUTIONARY RELATIONSHIP: AN APPLICATION OF MATHEMATICS IN MOLECULAR BIOLOGY

COSMOS ◽  
2005 ◽  
Vol 01 (01) ◽  
pp. 29-45
Author(s):  
A. D. BARBOUR
Keyword(s):  
Molecular Biology ◽  
Theoretical Analysis ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Biological Applications ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Mathematical Problems

The paper illustrates some mathematical problems that are motivated by molecular biological applications and the techniques that are used to address them. The context is that of detecting evolutionary relationship on the basis of molecular sequence data and of measuring its strength. The Stein–Chen method is shown to play a central role in the theoretical analysis of many of the procedures used in practice.

scholarly journals Phylogenetic study and taxonomic revision of the Xanthoparmelia mexicana group, including the description of a new species (Parmeliaceae, Ascomycota)

MycoKeys ◽  
2018 ◽  
Vol 40 ◽  
pp. 13-28 ◽  
Author(s):  
Alejandrina Barcenas-Peña ◽  
Steven D. Leavitt ◽  
Jen-Pan Huang ◽  
Felix Grewe ◽  
H. Thorsten Lumbsch
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Taxonomic Revision ◽  
Phylogenetic Study ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Unknown Substance ◽  
History Of ◽  
Taxonomic Implications ◽  
A New Species

Xanthoparmelia(Parmeliaceae, Ascomycota) is the most species-rich genus of lichen-forming fungi. Species boundaries are based on morphological and chemical features, varying reproductive strategies and, more recently, molecular sequence data. The isidiateXanthoparmeliamexicanagroup is common in arid regions of North and Central America and includes a range of morphological variation and variable secondary metabolites – salazinic or stictic acids mainly. In order to better understand the evolutionary history of this group and potential taxonomic implications, a molecular phylogeny representing 58 ingroup samples was reconstructed using four loci, including ITS, mtSSU, nuLSU rDNA and MCM7. Results indicate the existence of multiple, distinct lineages phenotypically agreeing withX.mexicana.One of these isidiate, salazinic acid-containing lineages is described here as a new species,X.pedregalensissp. nov., including populations from xerophytic scrub vegetation in Pedregal de San Angel, Mexico City.X.mexicanas. str. is less isidiate thanX.pedregalensisand has salazinic and consalazinic acid, occasionally with norstictic acid; whereasX.pedregalensiscontains salazinic and norstictic acids and an unknown substance. Samples from the Old World, morphologically agreeing withX.mexicana, are only distantly related toX.mexicanas. str. Our results indicate thatX.mexicanais likely less common than previously assumed and ongoing taxonomic revisions are required for isidiateXanthoparmeliaspecies.

scholarly journals Very few sites can reshape a phylogenetic tree

2018 ◽  
Author(s):  
Warren R. Francis ◽  
Donald E. Canfield
Keyword(s):  
Sequence Data ◽  
Acid Sites ◽  
Entire Genome ◽  
Animal Evolution ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Relative Placement ◽  
Gene Sets ◽  
Animal Phyla ◽  
History Of

AbstractThe history of animal evolution, and the relative placement of extant animal phyla in this history is, in principle, testable from phylogenies derived from molecular sequence data. Though datasets have increased in size and quality in the past years, the contribution of individual genes (and ultimately amino acid sites) to the final phylogeny is unequal across genes. Here we demonstrate that by removing a small fraction of sites that strongly favor one topology, it is possible produce a highly-supported tree of an alternate topology. We explore this approach using a dataset for animal phylogeny, and create a highly-supported tree with a monophyletic group of sponges and ctenophores, a topology not usually recovered. As nearly all gene sets are neither standardized nor representative of the entire genome, we conclude that there are only two possible ways to remedy this problem. One solution would need to use a fixed set of genes, which though not representative, is at least standardized. The other would be to construct phylogenies using all genes, thus limiting analysis to species with sequenced genomes.

The status of Myriangiaceae (Dothideomycetes)

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 219 ◽  
Author(s):  
ASHA J. DISSANAYAKE ◽  
RUVISHIKA S. JAYAWARDENA ◽  
SARANYAPHAT BOONMEE ◽  
KASUN M. THAMBUGALA ◽  
QING TIAN ◽  
...  
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
The Status ◽  
Sexual State ◽  
Morphological And Molecular Data ◽  
Asexual State ◽  
Molecular Characters

The family Myriangiaceae is relatively poorly known amongst the Dothideomycetes and includes genera which are saprobic, epiphytic and parasitic on the bark, leaves and branches of various plants. The family has not undergone any recent revision, however, molecular data has shown it to be a well-resolved family closely linked to Elsinoaceae in Myriangiales. Both morphological and molecular characters indicate that Elsinoaceae differs from Myriangiaceae. In Elsinoaceae, small numbers of asci form in locules in light coloured pseudostromata, which form typical scab-like blemishes on leaf or fruit surfaces. The coelomycetous, “Sphaceloma”-like asexual state of Elsinoaceae, form more frequently than the sexual state; conidiogenesis is phialidic and conidia are 1-celled and hyaline. In Myriangiaceae, locules with single asci are scattered in a superficial, coriaceous to sub-carbonaceous, black ascostromata and do not form scab-like blemishes. No asexual state is known. In this study, we revisit the family Myriangiaceae, and accept ten genera, providing descriptions and discussion on the generic types of Anhellia, Ascostratum, Butleria, Dictyocyclus, Diplotheca, Eurytheca, Hemimyriangium, Micularia, Myriangium and Zukaliopsis. The genera of Myriangiaceae are compared and contrasted. Myriangium duriaei is the type species of the family, while Diplotheca is similar and may possibly be congeneric. The placement of Anhellia in Myriangiaceae is supported by morphological and molecular data. Because of similarities with Myriangium, Ascostratum (A. insigne), Butleria (B. inaghatahani), Dictyocyclus (D. hydrangea), Eurytheca (E. trinitensis), Hemimyriangium (H. betulae), Micularia (M. merremiae) and Zukaliopsis (Z. amazonica) are placed in Myriangiaceae. Molecular sequence data from fresh collections is required to confirm the relationships and placement of the genera in this family.

Apertochrysa (Neuroptera: Chrysopidae): A heterogeneric phantom? 

Zootaxa ◽  
2017 ◽  
Vol 4238 (1) ◽  
pp. 58 ◽  
Author(s):  
ATSUSHI MOCHIZUKI ◽  
CHARLES S. HENRY ◽  
PETER DUELLI
Keyword(s):  
Type Species ◽  
Morphological Traits ◽  
New Genus ◽  
Sequence Data ◽  
New Combination ◽  
Wing Venation ◽  
Monophyletic Clade ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Group Relationships

The small lacewing genus Apertochrysa comprises species from Africa, Asia and Australia. All lack a tignum, but otherwise resemble distantly related genera. We show that Apertochrysa does not form a monophyletic clade, based on analyses of molecular sequence data and morphological traits such as the presence and shape of the male gonapsis, wing venation, and larval setae. Apertochrysa kichijoi forms a clade with Eremochrysa, Suarius and Chrysemosa, whereas A. albolineatoides belongs to a clade that includes Cunctochrysa. Apertochrysa albolineatoides should become a new combination as Cunctochrysa albolineatoides, while A. kichijoi will have to be transferred to a new genus. The Australian A. edwardsi, the African A. eurydera and the type species of the genus Apertochrysa, A. umbrosa, join the large Pseudomallada group. Relationships of A. umbrosa are less certain, because for it we could amplify only one of the three nuclear genes used in the overall analysis. However, in all morphological traits tested, that species strongly resembles A. edwardsi and A. eurydera and thus is very likely just another exceptional Pseudomallada lacking a tignum. The fate of the genus name Apertochrysa depends on additional molecular and morphological analyses of A. umbrosa. 

scholarly journals The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

2009 ◽  
Vol 364 (1527) ◽  
pp. 2197-2207 ◽  
Author(s):  
Peter G. Foster ◽  
Cymon J. Cox ◽  
T. Martin Embley
Keyword(s):  
Sequence Data ◽  
Phylogenetic Signal ◽  
Amino Acid Sequences ◽  
Rate Variation ◽  
Molecular Sequence Data ◽  
Protein Coding ◽  
Molecular Sequence ◽  
Heterogeneous Models ◽  
Matrix Heterogeneity ◽  
Rna Genes

The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the ‘eocyte hypothesis’, where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.

Revealing the endophytic mycoflora in tea (Camellia sinensis) leaves in Sri Lanka: the first comprehensive study

Phytotaxa ◽  
2021 ◽  
Vol 514 (3) ◽  
pp. 247-260
Author(s):  
KASUN THAMBUGALA ◽  
DINUSHANI DARANAGAMA ◽  
SAGARIKA KANNANGARA ◽  
THENUKA KODITUWAKKU
Keyword(s):  
Sri Lanka ◽  
Camellia Sinensis ◽  
Endophytic Fungi ◽  
Sequence Data ◽  
Fungal Endophytes ◽  
Fungal Endophyte ◽  
Tea Leaves ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Rdna Sequence Data

Endophytic fungi are a diverse group of microorganisms that live asymptomatically in healthy tissues of host and they have been reported from all kinds of plant tissues such as leaves, stems, roots, flowers, and fruits. In this study, fungal endophytes associated with tea leaves (Camellia sinensis) were collected from Kandy, Kegalle, and Nuwara Eliya districts in Sri Lanka and were isolated, characterized, and identified. A total of twenty endophytic fungal isolates belonging to five genera were recovered and ITS-rDNA sequence data were used to identify them. All isolated endophytic fungal strains belong to the phylum Ascomycota and the majority of these isolates were identified as Colletotrichum species. Phyllosticta capitalensis was the most commonly found fungal endophyte in tea leaves and was recorded in all three districts where the samples were collected. This is the very first investigation on fungal endophytes associated with C. sinensis in Sri Lanka based on molecular sequence data. In addition, a comprehensive account of known endophytic fungi reported worldwide on Camellia sinensis is provided.

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