Evolutionary Dynamics of Mating-Type Loci of Mycosphaerella spp. Occurring on Banana

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.

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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 ◽

10.1186/1471-2164-6-165 ◽

2005 ◽

Vol 6 (1) ◽

Cited By ~ 6

Author(s):

Peter ND Hunt ◽

Michael D Wilson ◽

Kristian R von Schalburg ◽

William S Davidson ◽

Ben F Koop

Keyword(s):

Evolutionary History ◽

Genomic Organization ◽

History Of ◽

Mosaic Protein ◽

Insight Into

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Insight into the evolutionary history of freshwater sponges: a new genus and new species of Spongillida (Porifera: Demospongiae) from Upper Cretaceous (Maastrichtian) Deccan intertrappean lacustrine deposits of the Malwa Group, Central India

Cretaceous Research ◽

10.1016/j.cretres.2021.104851 ◽

2021 ◽

pp. 104851

Author(s):

Bandana Samant ◽

Roberto Pronzato ◽

Dhananjay Mahendrakumar Mohabey ◽

Deepesh Kumar ◽

Anup Dhobale ◽

...

Keyword(s):

New Species ◽

Evolutionary History ◽

Upper Cretaceous ◽

New Genus ◽

Central India ◽

Freshwater Sponges ◽

Lacustrine Deposits ◽

History Of ◽

Insight Into

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The amphibamiform Nanobamus macrorhinus from the early Permian of Texas

Journal of Paleontology ◽

10.1017/jpa.2019.72 ◽

2019 ◽

Vol 94 (2) ◽

pp. 366-377 ◽

Cited By ~ 2

Author(s):

Bryan M. Gee ◽

Robert R. Reisz

Keyword(s):

Phylogenetic Analysis ◽

Evolutionary History ◽

Phylogenetic Position ◽

Early Permian ◽

Larval Form ◽

Terrestrial Environments ◽

History Of ◽

Insight Into

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.

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Ancient origins and multiple appearances of carotenoid-pigmented feathers in birds

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.0806 ◽

2014 ◽

Vol 281 (1788) ◽

pp. 20140806 ◽

Cited By ~ 41

Author(s):

Daniel B. Thomas ◽

Kevin J. McGraw ◽

Michael W. Butler ◽

Matthew T. Carrano ◽

Odile Madden ◽

...

Keyword(s):

Raman Spectroscopy ◽

High Performance ◽

Evolutionary History ◽

Carotenoid Pigments ◽

Biological Functions ◽

The Family ◽

Family Level ◽

History Of ◽

Living Species ◽

Insight Into

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.

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Evolutionary history of phycoerythrin pigmentation in the water bloom-forming cyanobacteriumMicrocystis aeruginosa

10.1101/485508 ◽

2018 ◽

Cited By ~ 2

Author(s):

Yuuhiko Tanabe ◽

Haruyo Yamaguchi

Keyword(s):

Evolutionary History ◽

Core Genome ◽

Genomic Organization ◽

Phylogenetic Analyses ◽

Green Light ◽

Water Bloom ◽

Phylogenetic Groups ◽

Genome Phylogeny ◽

History Of ◽

Genomic Basis

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.

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Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)

10.21203/rs.3.rs-154608/v1 ◽

2021 ◽

Author(s):

Xiaojin Liu ◽

Daping Xu ◽

Zhou Hong ◽

Ningnan Zhang ◽

Zhiyi Cui

Keyword(s):

Chloroplast Genome ◽

Evolutionary Dynamics ◽

Divergence Time ◽

Major Type ◽

Time Analysis ◽

Chloroplast Genomes ◽

Extant Species ◽

History Of ◽

Insight Into ◽

Simple Sequence

Abstract Background Santalum (Santalaceae, sandalwood) is a hemiparasitic genus including approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of the phylogenetic relationships and genetic diversity will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate the chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. Results The Santalum chloroplast genome contains the typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 124 genes. The whole set of ndh genes and the infA gene were found to lose their function. Between 17 and 31 SSRs were found in the Santalum chloroplast genome, and mononucleotide simple sequence repeats (SSRs) were the major type. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Our phylogenomic assessment provides improved resolution compared to past analyses. Our divergence time analysis shows that the crown age of Santalum was 8.46 Mya, the first divergence occurred around 6.97 Mya, and diversification was complete within approximately 1 Mya. Conclusions By sequencing the 12 chloroplast genomes of Santalum, we gain insight into the evolution of its chloroplast genomes. The chloroplast genome sequences had sufficient polymorphic information to elucidate the evolutionary history of Santalum.

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Evolution of a chordate-specific mechanism for myoblast fusion

10.1101/2021.07.24.453587 ◽

2021 ◽

Author(s):

Haifeng Zhang ◽

Renjie Shang ◽

Kwantae Kim ◽

Wei Zheng ◽

Christopher J. Johnson ◽

...

Keyword(s):

Evolutionary History ◽

De Novo ◽

Myoblast Fusion ◽

Last Common Ancestor ◽

Functional Tests ◽

Evolutionary Origins ◽

New Genes ◽

History Of ◽

Early Vertebrates ◽

And Function

The size of an animal is determined by the size of its musculoskeletal system. Myoblast fusion is an innovative mechanism that allows for multinucleated muscle fibers to compound the size and strength of individual mononucleated cells. However, the evolutionary history of the control mechanism underlying this important process is currently unknown. The phylum Chordata hosts closely related groups that span distinct myoblast fusion states: no fusion in cephalochordates, restricted fusion and multinucleation in tunicates, and extensive, obligatory fusion in vertebrates. To elucidate how these differences may have evolved, we studied the evolutionary origins and function of membrane-coalescing agents Myomaker and Myomixer in various groups of chordates. Here we report that Myomaker likely arose through gene duplication in the last common ancestor of tunicates and vertebrates, while Myomixer appears to have evolved de novo in early vertebrates. Functional tests revealed an unexpectedly complex evolutionary history of myoblast fusion in chordates. A pre-vertebrate phase of muscle multinucleation driven by Myomaker was followed by the later emergence of Myomixer that enables the highly efficient fusion system of vertebrates. Thus, our findings reveal the evolutionary origins of chordate-specific fusogens and illustrate how new genes can shape the emergence of novel morphogenetic traits and mechanisms.

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Approximating the coalescent under facultative sex

10.1101/846568 ◽

2019 ◽

Author(s):

Matthew Hartfield

Keyword(s):

Population Size ◽

Evolutionary History ◽

Sampling Strategies ◽

Effective Population ◽

Sexual Species ◽

History Of ◽

Mitotic Gene Conversion ◽

Evolutionary Consequences ◽

Insight Into ◽

Coalescent Time

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.

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Biological evolution

10.1093/oso/9780198808282.003.0012 ◽

2018 ◽

Author(s):

Andrew Briggs ◽

Hans Halvorson ◽

Andrew Steane

Keyword(s):

Design Education ◽

Evolutionary Biology ◽

Evolutionary History ◽

Biological Evolution ◽

Sequence Of Events ◽

Living Things ◽

History Of ◽

Informed Opinion ◽

Life On Earth ◽

Insight Into

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.

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