scholarly journals Expression and genomic organization of zonadhesin-like genes in three species of fish give insight into the evolutionary history of a mosaic protein

BMC Genomics ◽  
2005 ◽  
Vol 6 (1) ◽  
Author(s):  
Peter ND Hunt ◽  
Michael D Wilson ◽  
Kristian R von Schalburg ◽  
William S Davidson ◽  
Ben F Koop
2009 ◽  
Vol 9 (1) ◽  
pp. 164-172 ◽  
Author(s):  
Mahdi Arzanlou ◽  
Pedro W. Crous ◽  
Lute-Harm Zwiers

ABSTRACT The devastating Sigatoka disease complex of banana is primarily caused by three closely related heterothallic fungi belonging to the genus Mycosphaerella: M. fijiensis, M. musicola, and M. eumusae. Previous phylogenetic work showing common ancestry led us to analyze the mating-type loci of these Mycosphaerella species occurring on banana. We reasoned that this might provide better insight into the evolutionary history of these species. PCR and chromosome-walking approaches were used to clone the mating-type loci of M. musicola and M. eumusae. Sequences were compared to the published mating-type loci of M. fijiensis and other Mycosphaerella spp., and a novel organization of the MAT loci was found. The mating-type loci of the examined Mycosphaerella species are expanded, containing two additional Mycosphaerella-specific genes in a unique genomic organization. The proteins encoded by these novel genes show a higher interspecies than intraspecies homology. Moreover, M. fijiensis, M. musicola, and M. eumusae contain two additional mating-type-like loci, containing parts of both MAT 1-1-1 and MAT 1-2-1. The data indicate that M. fijiensis, M. musicola, and M. eumusae share an ancestor in which a fusion event occurred between MAT 1-1-1 and MAT 1-2-1 sequences and in which additional genes became incorporated into the idiomorph. The new genes incorporated have since then evolved independently in the MAT1-1 and MAT1-2 loci. Thus, these data are an example of the evolutionary dynamics of fungal MAT loci in general and show the great flexibility of the MAT loci of Mycosphaerella species in particular.


2019 ◽  
Vol 94 (2) ◽  
pp. 366-377 ◽  
Author(s):  
Bryan M. Gee ◽  
Robert R. Reisz

AbstractNanobamus macrorhinus Schoch and Milner, 2014 is a small amphibamiform temnospondyl from the early Permian Arroyo Formation of Texas. It is most readily characterized by an elongate and partially subdivided naris. This condition is superficially reminiscent of that seen in the coeval trematopids, the group to which N. macrorhinus was originally referred to under an interpretation of the holotype as a larval form. This was discounted by later workers, but the amphibamiform affinities of the specimen were not formalized until recently. The specimen has never been described in the context of its amphibamiform affinities and remains poorly characterized, never having been sampled in a phylogenetic analysis. Here we present a complete, updated osteological description of N. macrorhinus, including an improved characterization of its unique mosaic of plesiomorphic and apomorphic features and clarification of the taxon's autapomorphies. Our analysis of the taxon's phylogenetic position within Amphibamiformes shows that N. macrorhinus was recovered as diverging after basal amphibamiforms, e.g., the micropholids, and before derived amphibamiforms, e.g., the amphibamids. This is supported by the unique mixture of retained plesiomorphies, e.g., nonforeshortened postparietals and an oval choana, and apomorphies, e.g., a narrow interorbital region and slender palatal rami of the pterygoid. These results reflect the complexity of terrestrial amphibamiform diversity and provide further insight into the evolutionary history of the lissamphibian stem in terrestrial environments.


2014 ◽  
Vol 281 (1788) ◽  
pp. 20140806 ◽  
Author(s):  
Daniel B. Thomas ◽  
Kevin J. McGraw ◽  
Michael W. Butler ◽  
Matthew T. Carrano ◽  
Odile Madden ◽  
...  

The broad palette of feather colours displayed by birds serves diverse biological functions, including communication and camouflage. Fossil feathers provide evidence that some avian colours, like black and brown melanins, have existed for at least 160 million years (Myr), but no traces of bright carotenoid pigments in ancient feathers have been reported. Insight into the evolutionary history of plumage carotenoids may instead be gained from living species. We visually surveyed modern birds for carotenoid-consistent plumage colours (present in 2956 of 9993 species). We then used high-performance liquid chromatography and Raman spectroscopy to chemically assess the family-level distribution of plumage carotenoids, confirming their presence in 95 of 236 extant bird families (only 36 family-level occurrences had been confirmed previously). Using our data for all modern birds, we modelled the evolutionary history of carotenoid-consistent plumage colours on recent supertrees. Results support multiple independent origins of carotenoid plumage pigmentation in 13 orders, including six orders without previous reports of plumage carotenoids. Based on time calibrations from the supertree, the number of avian families displaying plumage carotenoids increased throughout the Cenozoic, and most plumage carotenoid originations occurred after the Miocene Epoch (23 Myr). The earliest origination of plumage carotenoids was reconstructed within Passeriformes, during the Palaeocene Epoch (66–56 Myr), and not at the base of crown-lineage birds.


2018 ◽  
Author(s):  
Yuuhiko Tanabe ◽  
Haruyo Yamaguchi

AbstractMicrocystis aeruginosais a bloom-forming cyanobacterium found in eutrophic fresh-and brackish water bodies worldwide. As typical for cyanobacteria, mostM. aeruginosastrains are blue-green in color owing to the concomitance of two photosynthetic pigments, phycocyanin (PC) and chlorophylla. Although less common,M. aeruginosastrains that are brownish in color owing to the presence of another pigment phycoerythrin (PE) have been documented. However, the genomic basis, phylogeny, and evolutionary origin of PE pigmentation inM. aeruginosahave only been poorly characterized until date. In the present study, we sequenced and characterized the genomes of five PE-containingM. aeruginosastrains. Putative PE synthesis and regulation genes (thecpecluster) were identified in all five sequenced genomes as well as in three previously publishedM. aeruginosagenomes. Of note, Absorption spectra indicated that the PE content, but not PC content, was markedly altered in response to availability of red/green light in all PE-containing strains. This was consistent with the presence ofccaS/ccaR, a hallmark of type II chromatic adapter, in thecpecluster. Phylogenetic analyses of core genome genes indicated that PE-containing genotypes were located in three different phylogenetic groups. In contrast, the genomic organization of thecpecluster was mostly conserved regardless of genomic background. Additionally, the phylogenies of PE genes were found to be congruent, consistent with the core genome phylogeny. A comparison of core genome and PE genes showed a similar level of genetic divergence between two PE-containing groups. These results suggest that genes responsible for PE pigmentation were introduced intoM. aeruginosaearly during evolution and were repeatedly lost thereafter possibly due to ecological adaptation. Additional horizontal gene transfer (HGT) later during evolution also contributed to the present phylogenetic distribution of PE inM. aeruginosa.


2019 ◽  
Author(s):  
Matthew Hartfield

AbstractGenome studies of facultative sexual species, which can either reproduce sexually or asexually, are providing insight into the evolutionary consequences of mixed reproductive modes. It is currently unclear to what extent the evolutionary history of facultative sexuals’ genomes can be approximated by the standard coalescent, and if a coalescent effective population size Ne exists. Here, I determine if and when these approximations can be made. When sex is frequent (occurring at a frequency much greater than 1/N per reproduction per generation, for N the actual population size), the underlying genealogy can be approximated by the standard coalescent, with a coalescent Ne ≈ N. When sex is very rare (at frequency much lower than 1/N), approximations for the pairwise coalescent time can be obtained, which is strongly influenced by the frequencies of sex and mitotic gene conversion, rather than N. However, these terms do not translate into a coalescent Ne. These results are used to discuss the best sampling strategies for investigating the evolutionary history of facultative sexual species.


Author(s):  
Andrew Briggs ◽  
Hans Halvorson ◽  
Andrew Steane

The chapter discusses the history of life on Earth, and the lessons to be learned from the neo-Darwinian synthesis of evolutionary biology. The long and complex sequence of events in the evolutionary history of life on Earth requires considered interpretation. The neo-Darwinian synthesis is well-supported by evidence and gives rich insight into this process, but does not itself furnish a complete explanation or understanding of living things. This is because a process of exploration can only explore; it cannot fully dictate and can only partially constrain what type of thing will be found. What is found is constrained by other considerations, such as what is possible, and what can make sense. A brief critique of some of Richard Dawkins’ work is given, and also of the movement known as ‘Intelligent Design’. Education policy is well served by a fair appraisal of informed opinion in this area.


Taxon ◽  
2011 ◽  
Vol 60 (5) ◽  
pp. 1295-1305 ◽  
Author(s):  
Arántzazu Molins ◽  
Gianluigi Bacchetta ◽  
Marcela Rosato ◽  
Josep A. Rosselló ◽  
Maria Mayol

Mammalia ◽  
2017 ◽  
Vol 81 (6) ◽  
Author(s):  
Ahmad Mahmoudi ◽  
Jamshid Darvish ◽  
Mansour Aliabadian ◽  
Faezeh Yazdani Moghaddam ◽  
Boris Kryštufek

AbstractOur aim in this study was to further the understanding of the taxonomic relationships and the evolutionary history of grey voles (subgenus


Yeast ◽  
2000 ◽  
Vol 1 (4) ◽  
pp. 283-293 ◽  
Author(s):  
Ross D. King ◽  
Andreas Karwath ◽  
Amanda Clare ◽  
Luc Dehaspe

The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on theM. tuberculosisandE. coligenomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function inM. tuberculosisand 24% of those inE. coli, with an estimated accuracy of 60–80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, convergent evolution and horizontal gene transfer. We identify rules that predict protein functional class even in the absence of detectable sequence or structural homology. These rules give insight into the evolutionary history ofM. tuberculosisandE. coli.


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