β-Defensin evolution: selection complexity and clues for residues of functional importance

2006 ◽  
Vol 34 (2) ◽  
pp. 257-262 ◽  
Author(s):  
C.A.M. Semple ◽  
K. Taylor ◽  
H. Eastwood ◽  
P.E. Barran ◽  
J.R. Dorin
Keyword(s):  
Positive Selection ◽  
Evolutionary History ◽  
Mammalian Genome ◽  
Functional Importance ◽  
Selective Pressures ◽  
History Of ◽  
Orthologous Loci ◽  
Window Approach ◽  
First Time ◽  
Evolutionary Lineages

We have examined the evolution of the genes at the major human β-defensin locus and the orthologous loci in a range of other primates and mammals. For the first time, these data allow us to examine selective episodes in the more recent evolutionary history of this locus as well as in the ancient past. We have used a combination of maximum-likelihood-based tests and a maximum-parsimony-based sliding window approach to give a detailed view of the varying modes of selection operating at this locus. We provide evidence for strong positive selection soon after the duplication of these genes within an ancestral mammalian genome. During the divergence of primates, however, variable selective pressures have acted on β-defensin genes in different evolutionary lineages, with episodes of both negative and, more rarely, positive selection. Positive selection appears to have been more common in the rodent lineage, accompanying the birth of novel rodent-specific β-defensin gene clades. Sites in the second exon have been subject to positive selection and, by implication, are important in functional diversity. A small number of sites in the mature human peptides were found to have undergone repeated episodes of selection in different primate lineages. Particular sites were consistently implicated by multiple methods at positions throughout the mature peptides. These sites are clustered at positions that are predicted to be important for the function of β-defensins.

scholarly journals Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

2019 ◽  
Vol 286 (1897) ◽  
pp. 20182929 ◽  
Author(s):  
Elena A. Ritschard ◽  
Robert R. Fitak ◽  
Oleg Simakov ◽  
Sönke Johnsen
Keyword(s):  
Signal Transduction ◽  
Positive Selection ◽  
G Protein ◽  
Evolutionary History ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Genomic Signatures ◽  
History Of ◽  
G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

scholarly journals Belowground Carbohydrate Reserves of Mature Southern Pines Reflect Seedling Strategy to Evolutionary History of Disturbance

Forests ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 653 ◽  
Author(s):  
Joshua Mims ◽  
Joseph O’Brien ◽  
Doug Aubrey
Keyword(s):  
Evolutionary History ◽  
Temporal Dynamics ◽  
Pinus Palustris ◽  
Life History Stage ◽  
Southern Pine ◽  
Mature Trees ◽  
Carbohydrate Reserves ◽  
Selective Pressures ◽  
Southern Pines ◽  
History Of

Carbohydrate reserves provide advantages for mature trees experiencing frequent disturbances; however, it is unclear if selective pressures operate on this characteristic at the seedling or mature life history stage. We hypothesized that natural selection has favored carbohydrate reserves in species that have an evolutionary history of frequent disturbance and tested this using three southern pine species that have evolved across a continuum of fire frequencies. Longleaf pine (Pinus palustris) roots exhibited higher maximum starch concentrations than slash (P. elliottii) and loblolly (P. taeda), which were similar. Longleaf also relied on starch reserves in roots more than slash or loblolly, depleting 64, 41, and 23 mg g−1 of starch, respectively, between seasonal maximum and minimum, which represented 52%, 45%, and 26% of reserves, respectively. Starch reserves in stems did not differ among species or exhibit temporal dynamics. Our results suggest that an evolutionary history of disturbance partly explains patterns of carbohydrate reserves observed in southern pines. However, similarities between slash and loblolly indicate that carbohydrate reserves do not strictly follow the continuum of disturbance frequencies among southern pine, but rather reflect the different seedling strategies exhibited by longleaf compared to those shared by slash and loblolly. We propose that the increased carbohydrate reserves in mature longleaf may simply be a relic of selective pressures imposed at the juvenile stage that are maintained through development, thus allowing mature trees to be more resilient and to recover from chronic disturbances such as frequent fire.

scholarly journals Tribalism Is Human Nature

2019 ◽  
Vol 28 (6) ◽  
pp. 587-592 ◽  
Author(s):  
Cory J. Clark ◽  
Brittany S. Liu ◽  
Bo M. Winegard ◽  
Peter H. Ditto
Keyword(s):  
Evolutionary History ◽  
Cognitive Biases ◽  
Meta Analysis ◽  
Human Cognition ◽  
Partisan Bias ◽  
Selective Pressures ◽  
Group Loyalty ◽  
History Of ◽  
The Common ◽  
Political Spectrum

Humans evolved in the context of intense intergroup competition, and groups comprised of loyal members more often succeeded than groups comprised of nonloyal members. Therefore, selective pressures have sculpted human minds to be tribal, and group loyalty and concomitant cognitive biases likely exist in all groups. Modern politics is one of the most salient forms of modern coalitional conflict and elicits substantial cognitive biases. The common evolutionary history of liberals and conservatives gives little reason to expect protribe biases to be higher on one side of the political spectrum than the other. This evolutionarily plausible null hypothesis has been supported by recent research. In a recent meta-analysis, liberals and conservatives showed similar levels of partisan bias, and several protribe cognitive tendencies often ascribed to conservatives (e.g., intolerance toward dissimilar other people) were found in similar degrees in liberals. We conclude that tribal bias is a natural and nearly ineradicable feature of human cognition and that no group—not even one’s own—is immune.

scholarly journals Non-trophic Functional Ecology of Vertebrate Teeth: A Review

2020 ◽  
Vol 60 (3) ◽  
pp. 665-675
Author(s):  
Courtney E Gorman ◽  
C Darrin Hulsey
Keyword(s):  
Comparative Studies ◽  
Evolutionary History ◽  
Functional Ecology ◽  
Developmental Genetics ◽  
Ecological Diversity ◽  
Functional Importance ◽  
Substantial Role ◽  
History Of

Synopsis Teeth are critical to the functional ecology of vertebrate trophic abilities, but are also used for a diversity of other non-trophic tasks. Teeth can play a substantial role in how animals move, manipulate their environment, positively interact with conspecifics, antagonistically interact with other organisms, and sense the environment. We review these non-trophic functions in an attempt to place the utility of human and all other vertebrate dentitions in a more diverse framework that emphasizes an expanded view of the functional importance and ecological diversity of teeth. In light of the extensive understanding of the developmental genetics, trophic functions, and evolutionary history of teeth, comparative studies of vertebrate dentitions will continue to provide unique insights into multi-functionality, many-to-one mapping, and the evolution of novel abilities.

Systematics of Senecio section Crociseris (Compositae, Senecioneae)

Phytotaxa ◽  
2015 ◽  
Vol 211 (1) ◽  
pp. 1 ◽  
Author(s):  
JOEL CALVO ◽  
INÉS ÁLVAREZ ◽  
CARLOS AEDO
Keyword(s):  
Central Asia ◽  
Evolutionary History ◽  
Morphological Characters ◽  
The Other ◽  
Distribution Maps ◽  
History Of ◽  
Perennial Herbs ◽  
First Time ◽  
Northwestern Africa ◽  
Shape And Size

The complexity of the evolutionary history of Senecio is reflected in its conflicted taxonomy. Within this genus, Senecio section Crociseris (Compositae, Senecioneae), a group of perennial herbs distributed in Europe, western and Central Asia, and northwestern Africa, was not fully revised. A worldwide revision of this section recognizing 28 species and eight subspecies is presented here. The main morphological characters revealed as useful for distinguishing between species are the number and shape of supplementary and involucral bracts, synflorescence architecture, indumentum, and the shape and size of leaves and achenes. In this new taxonomic treatment S. provincialis and S. lagascanus have been segregated from S. doronicum, within which three subspecies are recognized (S. doronicum subsp. orientalis is validly published herein). On the other hand, S. ruthenensis from France and S. lusitanicus from Portugal have been synonymized to S. lagascanus, as well as S. ovatifolius, S. pisidicus, and S. tmoleus from Anatolia to S. kolenatianus, S. olympicus, and S. castagneanus respectively, S. bertramii from Lebanon to S. cilicius, and S. delbesianus from Syria to S. racemosus subsp. racemosus. Sixty eight names are lectotypified, the names S. barrelieri, S. pyrenaicus, and S. scopolii are neotypified, and one epitype is designated for the name S. perralderianus. Descriptions and distribution maps are provided for all the species included, as well as an identification key. Nine species are illustrated for the first time.

scholarly journals Conflicts with diarrheal pathogens trigger rapid evolution of an intestinal signaling axis

2020 ◽  
Author(s):  
Clayton M. Carey ◽  
Sarah E. Apple ◽  
Zoё A. Hilbert ◽  
Michael S. Kay ◽  
Nels C. Elde
Keyword(s):  
Positive Selection ◽  
Rapid Evolution ◽  
Genetic Conflict ◽  
Selective Pressures ◽  
Heat Stable ◽  
Guanylate Cyclase C ◽  
Signaling Axis ◽  
History Of ◽  
Water Secretion

AbstractThe pathogenesis of infectious diarrheal diseases is largely attributed to enterotoxin proteins that disrupt intestinal water absorption, causing severe dehydration. Despite profound health consequences, the impacts of diarrhea-causing microbes on the evolutionary history of host species are largely unknown. We investigated patterns of genetic variation in mammalian Guanylate Cyclase-C (GC-C), an intestinal receptor frequently targeted by bacterial enterotoxins, to determine how hosts might adapt in response to diarrheal infections. Under normal conditions, GC-C interacts with endogenous guanylin peptides to promote water secretion in the intestine, but signaling can be hijacked by bacterially-encoded heat-stable enterotoxins (STa) during infection, which leads to overstimulation of GC-C and diarrhea. Phylogenetic analysis in mammals revealed evidence of recurrent positive selection in the GC-C ligand-binding domain in primates and bats, consistent with selective pressures to evade interactions with STa. Using in vitro assays and transgenic intestinal organoids to model STa-mediated diarrhea, we show that GC-C diversification in these lineages results in substantial variation in toxin susceptibility. In bats, we observe a unique pattern of compensatory coevolution in the endogenous GC-C ligand uroguanylin, reflecting intense bouts of positive selection at the receptor-ligand interface. These findings demonstrate control of water physiology as a previously unrecognized interface for genetic conflict and reveal diarrheal pathogens as a source of selective pressure among diverse mammals.

scholarly journals A distinct expression profile in the cerebellum and striatum for genes under selection within introgression deserts

2021 ◽  
Author(s):  
Raul Buisan ◽  
Juan Moriano ◽  
Alejandro Andirko ◽  
Cedric Boeckx
Keyword(s):  
Positive Selection ◽  
Evolutionary History ◽  
Developmental Stages ◽  
Homo Sapiens ◽  
Transcriptomic Data ◽  
Functional Differences ◽  
History Of ◽  
Genomic Regions ◽  
Cerebral Neocortex

Analyses of ancient DNA from extinct hominins have provided unique insights into the complex evolutionary history of Homo sapiens, intricately related to that of the Neanderthals and the Denisovans as revealed by several instances of admixture events. These analyses have also allowed the identification of introgression deserts: genomic regions in our species that are depleted of `archaic' haplotypes. The presence of genes like FOXP2 in these deserts has been taken to be suggestive of brain-related functional differences between Homo species. Here, we seek a deeper characterization of these regions, taking into account signals of positive selection in our lineage. Analyzing publicly available transcriptomic data from the human brain at different developmental stages, we found that structures outside the cerebral neocortex, and especially the cerebellum and the striatum at prenatal stages, show the most divergent transcriptomic profiles when considering genes under positive selection within introgression deserts.

scholarly journals Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance

PLoS Genetics ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. e1009919
Author(s):  
Manuel Ares-Arroyo ◽  
Eduardo P. C. Rocha ◽  
Bruno Gonzalez-Zorn
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Evolutionary History ◽  
Hidden Markov ◽  
Bacteriocin Production ◽  
Antimicrobial Resistance Genes ◽  
History Of ◽  
Functional Shift ◽  
First Time

Antimicrobial resistance is one of the major threats to Public Health worldwide. Understanding the transfer and maintenance of antimicrobial resistance genes mediated by mobile genetic elements is thus urgent. In this work, we focus on the ColE1-like plasmid family, whose distinctive replication and multicopy nature has given rise to key discoveries and tools in molecular biology. Despite being massively used, the hosts, functions, and evolutionary history of these plasmids remain poorly known. Here, we built specific Hidden Markov Model(HMM) profiles to search ColE1 replicons within genomes. We identified 1,035 ColE1 plasmids in five Orders of γ-Proteobacteria, several of which are described here for the first time. The phylogenetic analysis of these replicons and their characteristic MOBP5/HEN relaxases suggest that ColE1 plasmids have diverged apart, with little transfer across orders, but frequent transfer across families. Additionally, ColE1 plasmids show a functional shift over the last decades, losing their characteristic bacteriocin production while gaining several antimicrobial resistance genes, mainly enzymatic determinants and including several extended-spectrum betalactamases and carbapenemases. Furthermore, ColE1 plasmids facilitate the intragenomic mobilization of these determinants, as various replicons were identified co-integrated with large non-ColE1 plasmids, mostly via transposases. These results illustrate how families of plasmids evolve and adapt their gene repertoires to bacterial adaptive requirements.

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