Fungi from the Rhynie chert: a view from the dark side

2003 ◽  
Vol 94 (4) ◽  
pp. 457-473 ◽  
Author(s):  
T. N. Taylor ◽  
S. D. Klavins ◽  
M. Krings ◽  
E. L. Taylor ◽  
H. Kerp ◽  
...  
Keyword(s):  
Fossil Record ◽  
Molecular Data ◽  
Host Responses ◽  
Dark Side ◽  
Early Devonian ◽  
Mycorrhizal Associations ◽  
Rhynie Chert ◽  
Complex Ecosystem ◽  
Taxonomic Groups ◽  
Fungal Interactions

ABSTRACTThe exquisite preservation of organisms in the Early Devonian Rhynie chert ecosystem has permitted the documentation of the morphology and life history biology of fungi belonging to several major taxonomic groups (e.g., Chytridiomycota, Ascomycota, Glomeromycota). The Rhynie chert also provides the first unequivocal evidence in the fossil record of fungal interactions that can in turn be compared with those in modern ecosystems. These interactions in the Rhynie chert involve both green algae and macroplants, with examples of saprophytism, parasitism, and mutualism, including the earliest mycorrhizal associations and lichen symbiosis known to date in the fossil record. Especially significant are several types of specific host responses to fungal infection that indicate that these plants had already evolved methods of defence similar and perhaps analogous to those of extant plants. This suggests that mechanisms underlying the establishment and sustenance of associations of fungi with land plants were well in place prior to the Early Devonian. In addition, a more complete understanding of the microbial organisms involved in this complex ecosystem can also provide calibration points for phylogenies based on molecular data analysis. The richness of the microbial community in the Rhynie chert holds tremendous potential for documenting additional fungal groups, which permits speculation about further interactions with abiotic and biotic components of the environment.

scholarly journals Major features of protistan evolution: controversies, problems and a few answers

2006 ◽  
Vol 29 (1) ◽  
pp. 55-80
Author(s):  
Jere H Lipps
Keyword(s):  
Fossil Record ◽  
Molecular Data ◽  
Trophic Levels ◽  
Early Earth ◽  
Huge Number ◽  
Geologic Time ◽  
Earth History ◽  
Important Development ◽  
Fossil Evidence

The major features of protist evolution are fraught with controversies, problems and few answers, especially in early Earth history. In general they are based on molecular data and fossil evidence that respectively provide a scaffold and details of eukaryotic phylogenetic and ecologic histories. 1. Their origin, inferred from molecular sequences, occurred very early (>;3Ga). They are a chimera of different symbiont-derived organelles, including possibly the nucleus. 2. The initial diversification of eukaryotes may have occurred early in geologic time. Six supergroups exist today, each with fossils known from the Proterozoic and Phanerozoic. 3. Sex, considered an important development, may have been inherited from bacteria. 4. Precambrian protists were largely pelagic cyst-bearing taxa, but benthic forms were probably quite diverse and abundant. 5. Protists gave rise to animals long before 600 Ma through the choanoflagellates, for which no fossil record exists. 6. Acritarchs and skeletonized protists radiated in the Cambrian (544-530 my). From then on, they radiated and became extinct at all the major events recorded in the metazoan fossil record. 7. Protists dominated major environments (shelves and reefs) starting with a significant radiation in the Ordovician, followed by extinctions and other radiations until most died out at the end of the Permian. 8. In the Mesozoic, new planktic protozoa and algae appeared and radiated in pelagic environments. 9. Modern protists are important at all trophic levels in the oceans and a huge number terrestrial, parasitic and symbiotic protists must have existed for much of geologic time as well. 10. The future of protists is likely in jeopardy, just like most reefal, benthic, and planktic metazoans. An urgent need to understand the role of protists in modern threatened oceans should be addressed soon.

scholarly journals Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4349 ◽  
Author(s):  
Aristóteles Góes-Neto ◽  
Marcelo V.C. Diniz ◽  
Daniel S. Carvalho ◽  
Gilberto C. Bomfim ◽  
Angelo A. Duarte ◽  
...  
Keyword(s):  
Biological Sciences ◽  
Phylogenetic Analysis ◽  
Complex Networks ◽  
Complex Network ◽  
Bootstrap Method ◽  
Molecular Data ◽  
Data Sets ◽  
Fungal Cell ◽  
Taxonomic Groups ◽  
Inference Methods

Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.

Countering Common Misconceptions of Evolution in the Paleontology Classroom

2012 ◽  
Vol 12 ◽  
pp. 109-122
Author(s):  
Keith B. Miller
Keyword(s):  
Fossil Record ◽  
Temporal Pattern ◽  
Historical Context ◽  
Evolutionary Trees ◽  
Teaching Evolution ◽  
New Knowledge ◽  
Evolutionary Science ◽  
Taxonomic Groups ◽  
Scientific Testing ◽  
Evolutionary Continuity

Students will come to class with misconceptions about evolution and about the nature of science itself. Erroneous views that create obstacles to teaching evolution include: 1) that the fossil record does not support evolutionary continuity between different taxonomic groups; 2) that the expected temporal pattern of evolution is linear and ladder-like; and 3) that evolutionary hypotheses are not subject to scientific testing. These views negatively impact the understanding of evolutionary science, particularly paleontology, in a number of ways. It is important that these misconceptions be recognized and explicitly countered. If student's false ideas are left unaddressed, new knowledge presented in the classroom will likely simply be superimposed on, or integrated with them. Effective teaching thus requires that we not only impart new knowledge, but seek to correct previously held false ideas. This essay presents several teaching strategies that can address misconceptions about evolution. These include: 1) teaching important concepts in their historical context; 2) having students construct and interpret cladograms; and 3) showing that, when interpreted as evolutionary trees, cladograms make testable predictions of the fossil record.

The first zosterophyll from the Lower Devonian Rhynie Chert, Aberdeenshire

1991 ◽  
Vol 82 (4) ◽  
pp. 324-332 ◽  
Author(s):  
A. G. Lyon ◽  
Dianne Edwards
Keyword(s):  
Lower Devonian ◽  
New Genus ◽  
New Genus And Species ◽  
Early Devonian ◽  
Precise Positioning ◽  
Cortical Zone ◽  
Lack Of Information ◽  
Rhynie Chert

ABSTRACTFragmentary remains of a vascular sporophyte from the Rhynie Chert are described as a new genus and species, Trichopherophyton teuchansii. The plant, which is characterised by the possession of unicellular spinous hairs, exarch xylem and laterally attached, marginally dehiscent sporangia, is assigned to the Zosterophyllophytina, but lack of information on the arrangement of sporangia prevents its more precise positioning within the subdivision. Unusual features include the combination of circinate tips to axes with almost terete xylem strands, and the lack of a thick-walled outer cortical zone. Associated axes, lacking spinous hairs, but having papillate or rhizoid-like epidermal emergences, are interpreted as likely rhizomes of Trichopherophyton. Features, such as unicellular spinous hairs, rhizoid-like emergences, circinate tipsand parenchymatous cortex are considered in relation to the functioning and growth of aplant inhabiting an early Devonian wetland.

scholarly journals Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny

2018 ◽  
Vol 285 (1893) ◽  
pp. 20181632 ◽  
Author(s):  
Robin M. D. Beck ◽  
Charles Baillie
Keyword(s):  
Maximum Likelihood ◽  
Fossil Record ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Case Scenario ◽  
State Reconstruction ◽  
Consensus View

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical ‘best case scenario’ by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record—specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus—may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.

A new crustacean from the Early Devonian Rhynie chert, Aberdeenshire, Scotland

2002 ◽  
Vol 93 (4) ◽  
pp. 355-382 ◽  
Author(s):  
Stephen R. Fayers ◽  
Nigel H. Trewin
Keyword(s):  
Hydrothermal Activity ◽  
The Body ◽  
Early Devonian ◽  
Rhynie Chert

ABSTRACTA new crustacean, Castracollis wilsonae is described from a loose block of the Early Devonian Rhynie chert, found in the vicinity of Rhynie, Aberdeenshire, Scotland. It differs markedly from Lepidocaris rhyniensis, Scourfield 1926, the only other crustacean found in the Rhynie chert.The material comprises complete individuals up to 8 mm long and fragmentary remains. The head is normally damaged and detached from the body, and damage to the anterior of the trunk suggests the specimens are exuviae. The head appears domed with a labrum, robust mandibles, and long biramous antennae. A few specimens exhibit a probable detached cephalo-thoracicshield. The trunk is multi-segmented, comprising similar ring-like somites. The thorax variably comprises up to 26 segments. The anterior 11 segments possess similar long, phyllopodous appendages, the remainder variably possess 10 to 15 phyllopodous appendages with a disposition of one per somite. The abdomen comprises up to 28 apodous segments. The posterior of the body comprises a telson with two furcal rami.The crustacean is most probably a calmanostracan branchiopod. It occurs associated with Lepidocaris, charophytes, cyanobacteria and coprolites within a ‘clotted’ chert texture, indicating subaqueous deposition, most probably in a temporary freshwater pool in an area of surficial hydrothermal activity.

scholarly journals Highlights in Seagrasses’ Phylogeny, Physiology, and Metabolism: What Makes Them Special?

ISRN Botany ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Jutta Papenbrock
Keyword(s):  
Molecular Data ◽  
Species Level ◽  
Terrestrial Plants ◽  
Open Questions ◽  
Physiological Adaptations ◽  
Paraphyletic Group ◽  
Points Of View ◽  
Taxonomic Groups

The marine seagrasses form an ecological and therefore paraphyletic group of marine hydrophilus angiosperms which evolved three to four times from land plants towards an aquatic and marine existence. Their taxonomy is not yet solved on the species level and below due to their reduced morphology. So far also molecular data did not completely solve the phylogenetic relationships. Thus, this group challenges a new definition for what a species is. Also their physiology is not well understood due to difficult experimental in situ and in vitro conditions. There remain several open questions concerning how seagrasses adapted secondarily to the marine environment. Here probably exciting adaptation solutions will be detected. Physiological adaptations seem to be more important than morphological ones. Seagrasses contain several compounds in their secondary metabolism in which they differ from terrestrial plants and also not known from other taxonomic groups. Some of these compounds might be of interest for commercial purposes. Therefore their metabolite contents constitute another treasure of the ocean. This paper gives an introduction into some of the most interesting aspects from phylogenetical, physiological, and metabolic points of view.

scholarly journals Morphology and molecular evaluation of Iphinoe spelaeobios gen. nov., sp. nov. and Loriellopsis cavernicola gen. nov., sp. nov., two stigonematalean cyanobacteria from Greek and Spanish caves

2011 ◽  
Vol 61 (12) ◽  
pp. 2907-2915 ◽  
Author(s):  
V. Lamprinou ◽  
M. Hernández-Mariné ◽  
T. Canals ◽  
K. Kormas ◽  
A. Economou-Amilli ◽  
...  
Keyword(s):  
Morphological Characteristics ◽  
Molecular Data ◽  
Rrna Gene ◽  
Genetic Traits ◽  
Transmission Electron ◽  
Different Strains ◽  
Taxonomic Groups ◽  
Type V ◽  
Micro Organisms

Caves have generally been found to host phototrophic micro-organisms from various taxonomic groups, with cyanobacteria comprising an important group that have adapted to these stable and highly specific environments. A polyphasic study based on aspects of classical morphology and molecular data revealed two new monospecific genera from fresh material of Greek and Spanish caves. Both taxa are characterized by obligatory true branching (T-type, V-type and false branching), the presence of heterocysts, and reproduction by hormocysts and akinetes. They shared some similarities in their morphological characteristics as revealed by light, scanning electron and transmission electron microscopy, but phylogenetic analysis based on 16S rRNA gene sequences showed that the two phylotypes were different (89.8 % similarity); this represents an example of shared morphology in genetically different strains of cave-adapted species. Phenotypic and genetic traits strongly support classification of the phylotypes as independent taxa in the order Stigonematales (the most differentiated and complicated group of cyanobacteria), family Loriellaceae Geitl 1925. Hence, the names Iphinoe spelaeobios Lamprinou and Pantazidou gen. nov., sp. nov. and Loriellopsis cavernicola Hernández-Mariné and Canals gen. nov., sp. nov. are proposed.

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