Evolutionary trajectories of tooth histology patterns in modern sharks (Chondrichthyes, Elasmobranchii)

We performed an exploratory analysis of the morphology of the cranium in the white olm (Proteus anguinus anguinus) and the black olm (P. a. parkelj) with micro-CT scanning and geometric morphometrics. The mudpuppy (Necturus maculosus) was used as an outgroup. The black olm falls outside the white olm morphospace by a markedly wider skull, shorter vomers which are positioned further apart and by laterally positioned squamosals and quadrates relative to the palate (the shape of the buccal cavity). On account of its robust skull with more developed premaxillae a shorter otico-occipital region, the black olm is positioned closer to Necturus than are the studied specimens of the white olm. The elongated skull of the white olm, with an anteriorly positioned jaw articulation point, could be regarded as an adaptation for improved feeding success, possibly compensating for lack of vision. As yet, the alternative explanations on the evolution of troglomorphism in Proteus are an extensive convergence in white olms versus the reverse evolution towards less troglomorphic character states in the black olm. To further understand the evolutionary trajectories within Proteus we highlight the following hypotheses for future testing: i) morphological differentiation is smaller within than between genetically differentiated white olm lineages, and ii) ontogenetic shape changes are congruent with the shape changes between lineages. We anticipate that the morphological detail and analytical power that come with the techniques we here employed will assist us in this task.

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Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia

Scientific Reports ◽

10.1038/s41598-021-95109-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shumaila Sayyab ◽

Anders Lundmark ◽

Malin Larsson ◽

Markus Ringnér ◽

Sara Nystedt ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

Large Scale ◽

Somatic Mutations ◽

Lymphoblastic Leukemia ◽

Clonal Evolution ◽

Point Mutations ◽

Driver Genes ◽

Protein Coding ◽

Pediatric Acute Lymphoblastic Leukemia ◽

Evolutionary Trajectories

AbstractThe mechanisms driving clonal heterogeneity and evolution in relapsed pediatric acute lymphoblastic leukemia (ALL) are not fully understood. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients. Somatic point mutations and large-scale structural variants were called using individually matched remission samples as controls, and allelic expression of the mutations was assessed in ALL cells using RNA-sequencing. We observed an increased burden of somatic mutations at relapse, compared to diagnosis, and at second relapse compared to first relapse. In addition to 29 known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, we identified putative non-protein coding mutations in regulatory regions of seven additional genes that have not previously been described in ALL. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression from diagnosis to relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.

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The Diversity and Evolution of Sex Chromosomes in Frogs

Genes ◽

10.3390/genes12040483 ◽

2021 ◽

Vol 12 (4) ◽

pp. 483

Author(s):

Wen-Juan Ma ◽

Paris Veltsos

Keyword(s):

Sex Determination ◽

Sex Chromosomes ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Comparative Genomic ◽

Ancestral State ◽

Heteromorphic Sex Chromosomes ◽

Genomic Studies ◽

Evolutionary Trajectories ◽

Heterogametic Sex

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

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CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes

Microbial Physiology ◽

10.1159/000516643 ◽

2021 ◽

pp. 1-16

Author(s):

Anca Butiuc-Keul ◽

Anca Farkas ◽

Rahela Carpa ◽

Dumitrana Iordache

Keyword(s):

Nucleic Acids ◽

Pathogenic Bacteria ◽

The Novel ◽

Defense System ◽

Guide Rnas ◽

Crispr Array ◽

Different Types ◽

Evolutionary Trajectories ◽

Novel Coronavirus ◽

Cas Proteins

Being frequently exposed to foreign nucleic acids, bacteria and archaea have developed an ingenious adaptive defense system, called CRISPR-Cas. The system is composed of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array, together with CRISPR (<i>cas</i>)-associated genes. This system consists of a complex machinery that integrates fragments of foreign nucleic acids from viruses and mobile genetic elements (MGEs), into CRISPR arrays. The inserted segments (spacers) are transcribed and then used by cas proteins as guide RNAs for recognition and inactivation of the targets. Different types and families of CRISPR-Cas systems consist of distinct adaptation and effector modules with evolutionary trajectories, partially independent. The origin of the effector modules and the mechanism of spacer integration/deletion is far less clear. A review of the most recent data regarding the structure, ecology, and evolution of CRISPR-Cas systems and their role in the modulation of accessory genomes in prokaryotes is proposed in this article. The CRISPR-Cas system's impact on the physiology and ecology of prokaryotes, modulation of horizontal gene transfer events, is also discussed here. This system gained popularity after it was proposed as a tool for plant and animal embryo editing, in cancer therapy, as antimicrobial against pathogenic bacteria, and even for combating the novel coronavirus – SARS-CoV-2; thus, the newest and promising applications are reviewed as well.

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Specific phenotypic, genomic, and fitness evolutionary trajectories toward streptomycin resistance induced by pesticide co-stressors in Escherichia coli

ISME Communications ◽

10.1038/s43705-021-00041-z ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Yue Xing ◽

Xiaoxi Kang ◽

Siwei Zhang ◽

Yujie Men

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Selective Pressure ◽

Fold Increase ◽

Streptomycin Resistance ◽

Evolutionary Stage ◽

Fitness Costs ◽

Evolutionary Trajectories ◽

K 12 ◽

Late Stages

AbstractTo explore how co-occurring non-antibiotic environmental stressors affect evolutionary trajectories toward antibiotic resistance, we exposed susceptible Escherichia coli K-12 populations to environmentally relevant levels of pesticides and streptomycin for 500 generations. The coexposure substantially changed the phenotypic, genotypic, and fitness evolutionary trajectories, resulting in much stronger streptomycin resistance (>15-fold increase) of the populations. Antibiotic target modification mutations in rpsL and rsmG, which emerged and dominated at late stages of evolution, conferred the strong resistance even with less than 1% abundance, while the off-target mutations in nuoG, nuoL, glnE, and yaiW dominated at early stages only led to mild resistance (2.5–6-fold increase). Moreover, the strongly resistant mutants exhibited lower fitness costs even without the selective pressure and had lower minimal selection concentrations than the mildly resistant ones. Removal of the selective pressure did not reverse the strong resistance of coexposed populations at a later evolutionary stage. The findings suggest higher risks of the selection and propagation of strong antibiotic resistance in environments potentially impacted by antibiotics and pesticides.

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Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles

The ISME Journal ◽

10.1038/s41396-021-01056-z ◽

2021 ◽

Author(s):

Gitta Szabó ◽

Frederik Schulz ◽

Alejandro Manzano-Marín ◽

Elena Rebecca Toenshoff ◽

Matthias Horn

Keyword(s):

Defense Mechanisms ◽

Amino Acid Production ◽

Evolutionary Transition ◽

Evolutionary Time ◽

Evolutionary Trajectories ◽

Host Infection ◽

Phylogenomic Analyses ◽

Time Specific ◽

High Level ◽

Metagenomic Approach

AbstractAdelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelgestardus species complex containing betaproteobacterial (“Candidatus Vallotia tarda”) and gammaproteobacterial (“Candidatus Profftia tarda”) symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other’s role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

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Plant evolution driven by interactions with symbiotic and pathogenic microbes

Science ◽

10.1126/science.aba6605 ◽

2021 ◽

Vol 371 (6531) ◽

pp. eaba6605 ◽

Cited By ~ 4

Author(s):

Pierre-Marc Delaux ◽

Sebastian Schornack

Keyword(s):

Cell Biology ◽

Genetic Basis ◽

Reverse Genetics ◽

Molecular Mechanisms ◽

Plant Evolution ◽

Symbiotic Microorganisms ◽

Protection Mechanisms ◽

Evolutionary Trajectories ◽

Microbe Interactions ◽

Pathogenic Microbes

During 450 million years of diversification on land, plants and microbes have evolved together. This is reflected in today’s continuum of associations, ranging from parasitism to mutualism. Through phylogenetics, cell biology, and reverse genetics extending beyond flowering plants into bryophytes, scientists have started to unravel the genetic basis and evolutionary trajectories of plant-microbe associations. Protection against pathogens and support of beneficial, symbiotic, microorganisms are sustained by a blend of conserved and clade-specific plant mechanisms evolving at different speeds. We propose that symbiosis consistently emerges from the co-option of protection mechanisms and general cell biology principles. Exploring and harnessing the diversity of molecular mechanisms used in nonflowering plant-microbe interactions may extend the possibilities for engineering symbiosis-competent and pathogen-resilient crops.

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Mistranslation can promote the exploration of alternative evolutionary trajectories in enzyme evolution

Journal of Evolutionary Biology ◽

10.1111/jeb.13892 ◽

2021 ◽

Author(s):

Jia Zheng ◽

Sinisa Bratulic ◽

Heidi E. L. Lischer ◽

Andreas Wagner

Keyword(s):

Enzyme Evolution ◽

Evolutionary Trajectories

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Effects of intra-gene fitness interactions on the benefit of sexual recombination

Biochemical Society Transactions ◽

10.1042/bst0340560 ◽

2006 ◽

Vol 34 (4) ◽

pp. 560-561 ◽

Cited By ~ 6

Author(s):

R.A. Watson ◽

D.M. Weinreich ◽

J. Wakeley

Keyword(s):

Nucleotide Sequence ◽

Point Mutation ◽

Sequence Space ◽

Fitness Effect ◽

Epistatic Interactions ◽

Genetic Sequence ◽

High Fitness ◽

Sexual Recombination ◽

Evolutionary Trajectories ◽

Asexual Populations

Whereas spontaneous point mutation operates on nucleotides individually, sexual recombination manipulates the set of nucleotides within an allele as an essentially particulate unit. In principle, these two different scales of variation enable selection to follow fitness gradients in two different spaces: in nucleotide sequence space and allele sequence space respectively. Epistasis for fitness at these two scales, between nucleotides and between genes, may be qualitatively different and may significantly influence the advantage of mutation-based and recombination-based evolutionary trajectories respectively. We examine scenarios where the genetic sequence within a gene strongly influences the fitness effect of a mutation in that gene, whereas epistatic interactions between sites in different genes are weak or absent. We find that, in cases where beneficial alleles of a gene differ from one another at several nucleotide sites, sexual populations can exhibit enormous benefit compared with asexual populations: not only discovering fit genotypes faster than asexual populations, but also discovering high-fitness genotypes that are effectively not evolvable in asexual populations.

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