Eukaryotic origins

The origin of the eukaryotes is a fundamental scientific question that for over 30 years has generated a spirited debate between the competing Archaea (or three domains) tree and the eocyte tree. As eukaryotes ourselves, humans have a personal interest in our origins. Eukaryotes contain their defining organelle, the nucleus, after which they are named. They have a complex evolutionary history, over time acquiring multiple organelles, including mitochondria, chloroplasts, smooth and rough endoplasmic reticula, and other organelles all of which may hint at their origins. It is the evolutionary history of the nucleus and their other organelles that have intrigued molecular evolutionists, myself included, for the past 30 years and which continues to hold our interest as increasingly compelling evidence favours the eocyte tree. As with any orthodoxy, it takes time to embrace new concepts and techniques.

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Extensive introgression and mosaic genomes of Mediterranean endemic lizards

Nature Communications ◽

10.1038/s41467-021-22949-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Weizhao Yang ◽

Nathalie Feiner ◽

Catarina Pinho ◽

Geoffrey M. While ◽

Antigoni Kaliontzopoulou ◽

...

Keyword(s):

Evolutionary History ◽

Mediterranean Islands ◽

The Past ◽

Island Endemics ◽

Extant Species ◽

Mediterranean Island ◽

History Of ◽

Entire History ◽

The Mediterranean ◽

The Mediterranean Basin

AbstractThe Mediterranean basin is a hotspot of biodiversity, fuelled by climatic oscillation and geological change over the past 20 million years. Wall lizards of the genus Podarcis are among the most abundant, diverse, and conspicuous Mediterranean fauna. Here, we unravel the remarkably entangled evolutionary history of wall lizards by sequencing genomes of 34 major lineages covering 26 species. We demonstrate an early (>11 MYA) separation into two clades centred on the Iberian and Balkan Peninsulas, and two clades of Mediterranean island endemics. Diversification within these clades was pronounced between 6.5–4.0 MYA, a period spanning the Messinian Salinity Crisis, during which the Mediterranean Sea nearly dried up before rapidly refilling. However, genetic exchange between lineages has been a pervasive feature throughout the entire history of wall lizards. This has resulted in a highly reticulated pattern of evolution across the group, characterised by mosaic genomes with major contributions from two or more parental taxa. These hybrid lineages gave rise to several of the extant species that are endemic to Mediterranean islands. The mosaic genomes of island endemics may have promoted their extraordinary adaptability and striking diversity in body size, shape and colouration, which have puzzled biologists for centuries.

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Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽

10.3390/v13050737 ◽

2021 ◽

Vol 13 (5) ◽

pp. 737

Author(s):

Issiaka Bagayoko ◽

Marcos Giovanni Celli ◽

Gustavo Romay ◽

Nils Poulicard ◽

Agnès Pinel-Galzi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Sierra Leone ◽

Evolutionary History ◽

Molecular Diversity ◽

Genomic Data ◽

Gene Recombination ◽

Necrosis Virus ◽

History Of ◽

Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

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Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau

Communications Biology ◽

10.1038/s42003-020-01154-2 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Jiekun He ◽

Siliang Lin ◽

Jiatang Li ◽

Jiehua Yu ◽

Haisheng Jiang

Keyword(s):

Tibetan Plateau ◽

Evolutionary History ◽

The Tibetan Plateau ◽

Change Over Time ◽

Deep Time ◽

Terrestrial Vertebrates ◽

History Of ◽

Striking Change ◽

Time Periods ◽

Over Time

AbstractThe Tibetan Plateau (TP) and surrounding regions have one of the most complex biotas on Earth. However, the evolutionary history of these regions in deep time is poorly understood. Here, we quantify the temporal changes in beta dissimilarities among zoogeographical regions during the Cenozoic using 4,966 extant terrestrial vertebrates and 1,278 extinct mammal genera. We identify ten present-day zoogeographical regions and find that they underwent a striking change over time. Specifically, the fauna on the TP was close to the Oriental realm in deep time but became more similar to the Palearctic realms more recently. The present-day zoogeographical regions generally emerged during the Miocene/Pliocene boundary (ca. 5 Ma). These results indicate that geological events such as the Indo-Asian Collision, the TP uplift, and the aridification of the Asian interior underpinned the evolutionary history of the zoogeographical regions surrounding the TP over different time periods.

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Rhizobial plasmids — replication, structure and biological role

Open Life Sciences ◽

10.2478/s11535-012-0058-8 ◽

2012 ◽

Vol 7 (4) ◽

pp. 571-586 ◽

Cited By ~ 8

Author(s):

Andrzej Mazur ◽

Piotr Koper

Keyword(s):

Genome Organization ◽

Soil Bacteria ◽

Evolutionary History ◽

Bacterial Genome ◽

Biological Role ◽

Genome Architecture ◽

Genomic Knowledge ◽

History Of ◽

Cryptic Plasmids ◽

Complex Evolutionary History

AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.

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Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life

American Journal of Botany ◽

10.1002/ajb2.1066 ◽

2018 ◽

Vol 105 (3) ◽

pp. 315-329 ◽

Cited By ~ 7

Author(s):

Hilary A. McManus ◽

Karolina Fučíková ◽

Paul O. Lewis ◽

Louise A. Lewis ◽

Kenneth G. Karol

Keyword(s):

Evolutionary History ◽

Tree Of Life ◽

Green Algal ◽

Plastid Genomes ◽

History Of ◽

Complex Evolutionary History

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A total evidence approach using palynological characters to infer the complex evolutionary history of the Asian Impatiens (Balsaminaceae)

Taxon ◽

10.1002/tax.612007 ◽

2012 ◽

Vol 61 (2) ◽

pp. 355-367 ◽

Cited By ~ 10

Author(s):

Steven B. Janssens ◽

Yi Song Wilson ◽

Yong-Ming Yuan ◽

Anne Nagels ◽

Erik F. Smets ◽

...

Keyword(s):

Evolutionary History ◽

Total Evidence ◽

History Of ◽

Complex Evolutionary History

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Toward an Institutional Theory of Community and Community Associations: a Review

Voluntaristics Review ◽

10.1163/24054933-12340027 ◽

2019 ◽

Vol 4 (1) ◽

pp. 1-63 ◽

Cited By ~ 2

Author(s):

Carl Milofsky

Keyword(s):

Social Capital ◽

Institutional Theory ◽

Urban Sociology ◽

Limited Liability ◽

Community Based ◽

Community Based Organizations ◽

The Past ◽

Community Associations ◽

History Of ◽

Over Time

AbstractThis article argues the position that the symbolic sense of community is a product of action by associations and larger community-based organizations. It draws on a theory from urban sociology called “the community of limited liability.” In the past this theory, first articulated by Morris Janowitz, has mostly been used to argue that residents living in a local neighborhood feel a sense of identification with that area to the extent that the symbolism of that neighborhood has been developed. This article extends Janowitz’s theory to apply to local associations and their efforts to create activities, movements, and products that encourage residents to expand their sense of symbolic attachment to a place. We argue that this organizational method has long been used by local associations but it has not been recognized as an organizational theory. Because associations have used this approach over time, communities have a historical legacy of organizing and symbol creating efforts by many local associations. Over time they have competed, collaborated, and together developed a collective vision of place. They also have created a local interorganizational field and this field of interacting associations and organizations is dense with what we call associational social capital. Not all communities have this history of associational activity and associational social capital. Where it does exist, the field becomes an institutionalized feature of the community. This is what we mean by an institutional theory of community.

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