Extensive duplication and convergent sequence evolution of an antimicrobial peptide gene

Mapping Intimacies ◽

10.1101/2021.02.24.432738 ◽

2021 ◽

Cited By ~ 1

Author(s):

M.A. Hanson ◽

B. Lemaitre

Keyword(s):

Evolutionary History ◽

Convergent Sequence ◽

Sequence Evolution ◽

Dual Roles ◽

Arms Races ◽

Repeated Events ◽

Encoding Gene ◽

Peptide Gene ◽

Recent Duplication

AbstractAntimicrobial peptides (AMPs) are host-encoded antibiotics that combat invading pathogens. AMPs are encoded by short genes that tend to evolve rapidly, likely responding to host-pathogen arms races. However recent studies have highlighted roles for AMPs in neurological contexts suggesting functions for these defence molecules beyond infection. Here we characterize the evolution of the Drosophila Baramicin (Bara) AMP gene family. We describe a recent duplication of the immune-induced BaraA locus, and trans-species polymorphisms in BaraA peptides that suggest dynamic selective pressures. We further recover multiple Baramicin paralogs in Drosophila melanogaster and other species, united by their N-terminal IM24 domain. Strikingly, some paralogs are no longer immune-induced. A careful dissection of the Baramicin family’s evolutionary history indicates that these non-immune paralogs result from repeated events of duplication and subsequent truncation of the coding sequence, leaving only the IM24 domain as the prominent gene product. Using mutation and targeted gene silencing, we demonstrate that two such genes are adapted for function in neural contexts in D. melanogaster. Using the Baramicin evolutionary history, we reveal unique properties of the different Baramicin domains. In doing so, we provide a case study for how an AMP-encoding gene might play dual roles in both immune and non-immune processes.

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Evolutionary history and species delimitations: a case study of the hazel dormouse, Muscardinus avellanarius

Conservation Genetics ◽

10.1007/s10592-016-0892-8 ◽

2016 ◽

Vol 18 (1) ◽

pp. 181-196 ◽

Cited By ~ 8

Author(s):

A. Mouton ◽

A. Mortelliti ◽

A. Grill ◽

M. Sara ◽

B. Kryštufek ◽

...

Keyword(s):

Evolutionary History ◽

Hazel Dormouse ◽

Muscardinus Avellanarius

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Evolutionary history predicts the response of tree species to forest loss: A case study in peninsular Spain

PLoS ONE ◽

10.1371/journal.pone.0204365 ◽

2018 ◽

Vol 13 (9) ◽

pp. e0204365 ◽

Cited By ~ 3

Author(s):

Rafael Molina-Venegas ◽

Sonia Llorente-Culebras ◽

Paloma Ruiz-Benito ◽

Miguel A. Rodríguez

Keyword(s):

Tree Species ◽

Evolutionary History ◽

Forest Loss ◽

Peninsular Spain

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Where Fossils Dare and Males Matter: combined morphological and molecular analysis untangles the evolutionary history of the spider ant genus Leptomyrmex Mayr (Hymenoptera : Dolichoderinae)

Invertebrate Systematics ◽

10.1071/is16067 ◽

2017 ◽

Vol 31 (6) ◽

pp. 765 ◽

Cited By ~ 3

Author(s):

Phillip Barden ◽

Brendon Boudinot ◽

Andrea Lucky

Keyword(s):

Evolutionary History ◽

Morphological Evolution ◽

Sister Group ◽

Morphological Characters ◽

Fossil Material ◽

First Case ◽

History Of ◽

The Impact ◽

Surprising Discovery

The distinctive ant genus Leptomyrmex Mayr, 1862 had been thought to be endemic to Australasia for over 150 years, but enigmatic Neotropical fossils have challenged this view for decades. The present study responds to a recent and surprising discovery of extant Leptomyrmex species in Brazil with a thorough evaluation of the Dominican Republic fossil material, which dates to the Miocene. In the first case study of direct fossil inclusion within Formicidae Latreille, 1809, we incorporated both living and the extinct Leptomyrmex species. Through simultaneous analysis of molecular and morphological characters in both Bayesian and parsimony frameworks, we recovered the fossil taxon as sister-group to extant Leptomyrmex in Brazil while considering the influence of taxonomic and character sampling on inferred hypotheses relating to tree topology, biogeography and morphological evolution. We also identified potential loss of signal in the binning of morphological characters and tested the impact of parameterisation on divergence date estimation. Our results highlight the importance of securing sufficient taxon sampling for extant lineages when incorporating fossils and underscore the utility of diverse character sources in accurate placement of fossil terminals. Specifically, we find that fossil placement in this group is influenced by the inclusion of male-based characters and the newly discovered Neotropical ‘Lazarus taxon’.

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Reconstructed protein sequence evolution consistent with the evolution of C4 photosynthesis via a C2 ancestor in the Paniceae

10.1101/733493 ◽

2019 ◽

Author(s):

Daniel S. Carvalho ◽

Sunil Kumar Kenchanmane Raju ◽

Yang Zhang ◽

James C. Schnable

Keyword(s):

Protein Sequence ◽

Evolutionary History ◽

C4 Photosynthesis ◽

Sequence Evolution ◽

Ancestral Branch ◽

History Of ◽

Grass Genomes ◽

Protein Sequence Evolution

AbstractThe grass tribe Paniceae includes a monophyletic subclade of species, the MPC clade, which specialize in each of the three primary C4 sub-pathways NADP-ME, NAD-ME and PCK. The evolutionary history of C4 photosynthesis in this subclade remains ambiguous. Leveraging newly sequenced grass genomes and syntenic orthology data, we estimated rates of protein sequence evolution on ancestral branches for both core enzymes shared across different C4 sub-pathways and enzymes specific to C4 sub-pathways. While core enzymes show elevated rates of protein sequence evolution in ancestral branches consistent with a transition from C3 to C4 photosynthesis in the ancestor for this clade, no subtype specific enzymes showed similar patterns. At least one protein involved in photorespiration also showed elevated rates of protein sequence evolution in the ancestral branch. The set of core C4 enzymes examined here combined with the photorespiratory pathway are necessary for the C2 photosynthetic cycle, a previously proposed intermediate between C3 and C4 photosynthesis. The patterns reported here are consistent with, but not conclusive proof that, C4 photosynthesis in the MPC clade of the Paniceae evolved via a C2 intermediate.

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Analyses of the core eukaryotic protein subunit of telomerase support extensive adaptation to different evolutionary and life histories in the Metazoa

10.1101/091124 ◽

2016 ◽

Author(s):

Alvina G. Lai ◽

Natalia Pouchkina-Stantcheva ◽

Alessia Di Donfrancesco ◽

Gerda Kildisiute ◽

Sounak Sahu ◽

...

Keyword(s):

Alternative Splicing ◽

Life Histories ◽

Evolutionary History ◽

Structural Evolution ◽

Sequence Evolution ◽

Dynamic Feature ◽

Protein Subunit ◽

Eukaryotic Protein ◽

Telomere Biology ◽

Splice Forms

AbstractMost animals employ telomerase, which consists of a catalytic subunit known as the telomerase reverse transcriptase (TERT) and an RNA template, to maintain telomere ends. Given the importance of TERT and the apparent importance of telomere biology in core metazoan life history traits like ageing and the control of somatic cell proliferation, we hypothesised that TERT would have patterns of sequence and regulatory evolution reflecting adaptations to diverse evolutionary and life histories across the Animal Kingdom. To test this, we performed a complete investigation of the evolutionary history of TERT across animals. We show that although TERT is almost ubiquitous across Metazoa, it has undergone substantial sequence evolution in canonical motifs. Beyond the known canonical motifs, we also identify and compare regions that are highly variable between lineages, but for which conservation exists within phyla. Recent data have highlighted the importance of alternate splice forms of TERT in non-canonical functions in some animals. Although animals may share some conserved introns, we find that the selection of exons for alternative splicing appears to be highly variable, and regulation by alternative splicing appears to be a very dynamic feature of TERT evolution. We show that even within a closely related group of triclad flatworms, where alternative splicing of TERT was previously correlated with reproductive strategy, we observe highly diverse alternative splicing patterns. Our work establishes that the evolutionary history and structural evolution of TERT involves previously unappreciated levels of change, supporting the view that this core eukaryotic protein has adapted to the requirements of diverse animal life histories.

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Distinguishing Biology from Geology in Soft-Tissue Preservation

The Paleontological Society Papers ◽

10.1017/s1089332600002898 ◽

2014 ◽

Vol 20 ◽

pp. 275-288 ◽

Cited By ~ 3

Author(s):

John A. Cunningham ◽

Philip C. J. Donoghue ◽

Stefan Bengtson

Keyword(s):

Soft Tissue ◽

Laser Beam ◽

Evolutionary History ◽

Soft Tissues ◽

Analytical Techniques ◽

Tissue Preservation ◽

Deep Time ◽

X Ray ◽

Soft Tissue Preservation

Knowledge of evolutionary history is based extensively on relatively rare fossils that preserve soft tissues. These fossils record a much greater proportion of anatomy than would be known solely from mineralized remains and provide key data for testing evolutionary hypotheses in deep time. Ironically, however, exceptionally preserved fossils are often among the most contentious because they are difficult to interpret. This is because their morphology has invariably been affected by the processes of decay and diagenesis, meaning that it is often difficult to distinguish preserved biology from artifacts introduced by these processes. Here we describe how a range of analytical techniques can be used to tease apart mineralization that preserves biological structures from unrelated geological mineralization phases. This approach involves using a series of X-ray, ion, electron and laser beam techniques to characterize the texture and chemistry of the different phases so that they can be differentiated in material that is difficult to interpret. This approach is demonstrated using a case study of its application to the study of fossils from the Ediacaran Doushantuo Biota.

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Emotion and Reason in Scientific Creation

The Poetry and Music of Science ◽

10.1093/oso/9780198797999.003.0006 ◽

2019 ◽

pp. 261-300

Author(s):

Tom McLeish

Keyword(s):

Jet Fuel ◽

Polymer Additive ◽

Medieval Philosophy ◽

Philosophical Discussion ◽

Dual Roles ◽

Cognition And Emotion ◽

Detailed Case ◽

Scientific Testimony

The dual roles of cognition and emotion in creativity that have emerged at many points in the book so far are examined in their own right. Through the lens of medieval philosophy, especially the work of Robert Grosseteste, then Kant, Spinoza, Hume, and the recent study of Iain McGilchrist, this chapter examines the structure of how the affective works in the origination of ideas, not just in response to them. Contemporary scientific testimony to the creative function of emotion leads to a detailed case study of a Caltech project to develop a polymer additive to make jet fuel safe in crashes, and other stories of scientific creation, earth the philosophical discussion in experience.

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