scholarly journals Evolutionary dynamics of circular RNAs in primates

2021 ◽  
Author(s):  
Gabriela Santos-Rodriguez ◽  
Irina Voineagu ◽  
Robert James Weatheritt
Keyword(s):  
Related Species ◽  
Evolutionary Dynamics ◽  
Expression Profiles ◽  
Primate Evolution ◽  
Circular Rnas ◽  
Species Identity ◽  
Closely Related Species ◽  
Tissue Specific ◽  
Comparative Analyses ◽  
Organ Type

Many primate genes produce noncoding circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. These circRNAs are defined by an extended downstream intron that has shown dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.

scholarly journals Evolutionary dynamics of circular RNAs in primates

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Gabriela Santos-Rodriguez ◽  
Irina Voineagu ◽  
Robert James Weatheritt
Keyword(s):  
Related Species ◽  
Evolutionary Dynamics ◽  
Expression Profiles ◽  
Primate Evolution ◽  
Circular Rnas ◽  
Species Identity ◽  
Closely Related Species ◽  
Tissue Specific ◽  
Organ Type ◽  
Species Specific

Many primate genes produce circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. By comparing to species-specific circRNAs, we identified that the downstream intron of the conserved circRNAs display a dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.

scholarly journals Recent Insights into Mechanisms of Genome Size Change in Plants

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Corrinne E. Grover ◽  
Jonathan F. Wendel
Keyword(s):  
Genome Size ◽  
Related Species ◽  
Evolutionary Dynamics ◽  
Higher Order ◽  
Size Change ◽  
Closely Related Species ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Recent Developments

Genome sizes vary considerably across all eukaryotes and even among closely related species. The genesis and evolutionary dynamics of that variation have generated considerable interest, as have the patterns of variation themselves. Here we review recent developments in our understanding of genome size evolution in plants, drawing attention to the higher order processes that can influence the mechanisms generating changing genome size.

scholarly journals Hybridization between Cutthroat and Rainbow Trout: Evidence from Biochemical Genetic Loci

1979 ◽  
Vol 3 ◽  
pp. 108-112
Author(s):  
Eric Loudenslager ◽  
G. Gall
Keyword(s):  
Rainbow Trout ◽  
Related Species ◽  
Cutthroat Trout ◽  
Salmo Gairdneri ◽  
Genetic Loci ◽  
Species Identity ◽  
Closely Related Species ◽  
Isolating Mechanisms ◽  
Biochemical Genetic ◽  
Salmo Clarki

Cutthroat, Salmo clarki, and rainbow, Salmo gairdneri, trout are largely allopatric, closely related species. Where naturally sympatric ecological isolating mechanisms maintain species identity. However, the inland subspecies of cutthroat trout which did not evolve in sympatry with rainbows are thought to freely hybridize with rainbow trout which have been introduced for recreational purposes. Because of the mass introductions of rainbow trout fish managers have become increasingly concerned about the purity of the dwindling stocks of native cutthroats.

Orthomnion elimbatum (Mniaceae, Bryophyta), a Malesian and Australian species new to China and Vietnam based on molecular data

Phytotaxa ◽  
2020 ◽  
Vol 451 (3) ◽  
pp. 206-214
Author(s):  
YAN-JUN YI ◽  
XIAO-XUAN XIAO ◽  
YAN LI ◽  
SI HE
Keyword(s):  
Molecular Analysis ◽  
Related Species ◽  
First Record ◽  
Molecular Data ◽  
Leaf Margin ◽  
Species Identity ◽  
Closely Related Species ◽  
Australian Species ◽  
Apical Leaf

Orthomnion elimbatum (Mniaceae) is herein reported new to China and Vietnam, representing the first record of the species northwards outside the Malesian and Australian regions. The species differs from the closely related species O. dilatatum by having undulate leaf margin, almost isodiametric laminal cells, and unbordered apical leaf margins. Confirmation of the species identity is validated by a molecular analysis based on rps4 and trnL-F sequences.

scholarly journals Transposable element dynamics are consistent across the Drosophila phylogeny, despite drastically differing content

2019 ◽  
Author(s):  
Tom Hill
Keyword(s):  
Drosophila Melanogaster ◽  
Related Species ◽  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Low Frequency ◽  
Fitness Costs ◽  
Closely Related Species ◽  
Drosophila Phylogeny ◽  
Turn Over ◽  
Insertion Frequency

AbstractBackgroundThe evolutionary dynamics of transposable elements (TEs) vary across the tree of life and even between closely related species with similar ecologies. In Drosophila, most of the focus on TE dynamics has been completed in Drosophila melanogaster and the overall pattern indicates that TEs show an excess of low frequency insertions, consistent with their frequent turn over and high fitness cost in the genome. Outside of D. melanogaster, insertions in the species Drosophila algonquin, suggests that this situation may not be universal, even within Drosophila. Here we test whether the pattern observed in D. melanogaster is similar across five Drosophila species that share a common ancestor more than fifty million years ago.ResultsFor the most part, TE family and order insertion frequency patterns are broadly conserved between species, supporting the idea that TEs have invaded species recently, are mostly costly and dynamics are conserved in orthologous regions of the host genomeConclusionsMost TEs retain similar activities and fitness costs across the Drosophila phylogeny, suggesting little evidence of drift in the dynamics of TEs across the phylogeny, and that most TEs have invaded species recently.

scholarly journals The spindle assembly checkpoint and speciation

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9073
Author(s):  
Robert C. Jackson ◽  
Hitesh B. Mistry
Keyword(s):  
Related Species ◽  
Spindle Assembly Checkpoint ◽  
Evolutionary Dynamics ◽  
Chromosomal Rearrangements ◽  
Spindle Assembly ◽  
Selective Advantage ◽  
Ecological Niches ◽  
Geographical Isolation ◽  
Closely Related Species ◽  
Definition Of

A mechanism is proposed by which speciation may occur without the need to postulate geographical isolation of the diverging populations. Closely related species that occupy overlapping or adjacent ecological niches often have an almost identical genome but differ by chromosomal rearrangements that result in reproductive isolation. The mitotic spindle assembly checkpoint normally functions to prevent gametes with non-identical karyotypes from forming viable zygotes. Unless gametes from two individuals happen to undergo the same chromosomal rearrangement at the same place and time, a most improbable situation, there has been no satisfactory explanation of how such rearrangements can propagate. Consideration of the dynamics of the spindle assembly checkpoint suggest that chromosomal fission or fusion events may occur that allow formation of viable heterozygotes between the rearranged and parental karyotypes, albeit with decreased fertility. Evolutionary dynamics calculations suggest that if the resulting heterozygous organisms have a selective advantage in an adjoining or overlapping ecological niche from that of the parental strain, despite the reproductive disadvantage of the population carrying the altered karyotype, it may accumulate sufficiently that homozygotes begin to emerge. At this point the reproductive disadvantage of the rearranged karyotype disappears, and a single population has been replaced by two populations that are partially reproductively isolated. This definition of species as populations that differ from other, closely related, species by karyotypic changes is consistent with the classical definition of a species as a population that is capable of interbreeding to produce fertile progeny. Even modest degrees of reproductive impairment of heterozygotes between two related populations may lead to speciation by this mechanism, and geographical isolation is not necessary for the process.

scholarly journals Tracing Genomic Divergence of Vibrio Bacteria in the Harveyi Clade

2018 ◽  
Vol 200 (15) ◽  
Author(s):  
Huei-Mien Ke ◽  
Dang Liu ◽  
Yoshitoshi Ogura ◽  
Tetsuya Hayashi ◽  
Henryk Urbanczyk ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Analyses ◽  
Gene Gain ◽  
Marine Animals ◽  
Evolutionary Mechanisms ◽  
Closely Related Species ◽  
Content Type ◽  
Comparative Analyses ◽  
Ecological Diversification ◽  
Study Results

ABSTRACT The mechanism of bacterial speciation remains a topic of tremendous interest. To understand the ecological and evolutionary mechanisms of speciation in Vibrio bacteria, we analyzed the genomic dissimilarities between three closely related species in the so-called Harveyi clade of the genus Vibrio, V. campbellii, V. jasicida, and V. hyugaensis. The analysis focused on strains isolated from diverse geographic locations over a long period of time. The results of phylogenetic analyses and calculations of average nucleotide identity (ANI) supported the classification of V. jasicida and V. hyugaensis into two species. These analyses also identified two well-supported clades in V. campbellii; however, strains from both clades were classified as members of the same species. Comparative analyses of the complete genome sequences of representative strains from the three species identified higher syntenic coverage between genomes of V. jasicida and V. hyugaensis than that between the genomes from the two V. campbellii clades. The results from comparative analyses of gene content between bacteria from the three species did not support the hypothesis that gene gain and/or loss contributed to their speciation. We also did not find support for the hypothesis that ecological diversification toward associations with marine animals contributed to the speciation of V. jasicida and V. hyugaensis. Overall, based on the results obtained in this study, we propose that speciation in Harveyi clade species is a result of stochastic diversification of local populations, which was influenced by multiple evolutionary processes, followed by extinction events. IMPORTANCE To investigate the mechanisms underlying speciation in the genus Vibrio, we provided a well-assembled reference of genomes and performed systematic genomic comparisons among three evolutionarily closely related species. We resolved taxonomic ambiguities and identified genomic features separating the three species. Based on the study results, we propose a hypothesis explaining how species in the Harveyi clade of Vibrio bacteria diversified.

scholarly journals Evolutionary dynamics of pre- and postzygotic reproductive isolation in cichlid fishes

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190535 ◽  
Author(s):  
Sina J. Rometsch ◽  
Julián Torres-Dowdall ◽  
Axel Meyer
Keyword(s):  
Reproductive Isolation ◽  
Related Species ◽  
Evolutionary Dynamics ◽  
Current Knowledge ◽  
Meta Analysis ◽  
Postzygotic Isolation ◽  
Ambient Conditions ◽  
Premating Isolation ◽  
Closely Related Species ◽  
Cichlid Fishes

Cichlid fishes are exceptionally species-rich, speciated at explosive rates and, hence, are a model system in speciation research. Yet, their reproductive isolating barriers have, so far, not been comprehensively studied. Here, we review current knowledge on pre- and postzygotic mechanisms in cichlids. While premating isolation is the norm in cichlids, its strength varies across lineages and with the geographical setting. Moreover, manipulations of ambient conditions tended to reduce assortative mating among closely related species, suggesting that premating isolation in cichlids is often fragile and context dependent. The observed lack of complete reproductive isolation is supported by past and present hybridization events that have contributed to diversity by creating novel allelic combinations. On the other hand, our meta-analysis highlights that intrinsic postzygotic isolation might accumulate faster than assumed. Mild forms of genetic incompatibilities, such as sex ratio distortion, can already be observed among closely related species. Therefore, cessation of gene flow by strong reproductive isolation in cichlids requires a combination of premating prezygotic isolation supplemented with intrinsic and extrinsic postzygotic barriers. Further, we suggest crucial next steps to improve our knowledge about reproductive barriers in cichlids to understand the evolutionary dynamics of pre- and postzygotic isolation mechanisms during adaptive radiations. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

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