Road Map to Study Convergent Evolution: A Proposition for Evolutionary Systems Biology Approaches

Pontarotti, Pierre; Hue, Isabelle

doi:10.1007/978-3-319-41324-2_1

Cited by 12 publications

(12 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another problem that prevented such observation is that authors do not make a clear distinction between allo-convergent and iso-convergent evolution even if the difference is sometimes mentioned by using the term of parallel evolution. However, as discussed by Pontarotti and Hue [ 1 ] the term is confusing, as some authors use this term to explain a morphological shift with the same genetic mechanisms.…”

Section: Enzyme Convergent Evolution Via Allo-convergent and Iso-cmentioning

confidence: 99%

“…In order to gain a finer-scale understanding of the dynamics of convergence, we proposed to use the concepts and corresponding terms “iso-convergent” and “allo-convergent” evolution [ 1 ]. Iso-convergent traits have converged from the same ancestral state (traditionally “parallel evolution” but parallel evolution also has a different meaning), whereas allo-convergent traits have converged from different ancestral states.…”

Section: Introduction: the Concepts: Iso And Allo-convergent Evolumentioning

confidence: 99%

See 1 more Smart Citation

Promiscuous Enzyme Activity as a Driver of Allo and Iso Convergent Evolution, Lessons from the β-Lactamases

Keshri

Chabrière

Pinault

et al. 2020

IJMS

Self Cite

View full text Add to dashboard Cite

The probability of the evolution of a character depends on two factors: the probability of moving from one character state to another character state and the probability of the new character state fixation. The more the evolution of a character is probable, the more the convergent evolution will be witnessed, and consequently, convergent evolution could mean that the convergent character evolution results as a combination of these two factors. We investigated this phenomenon by studying the convergent evolution of biochemical functions. For the investigation we used the case of β-lactamases. β-lactamases hydrolyze β-lactams, which are antimicrobials able to block the DD-peptidases involved in bacterial cell wall synthesis. β-lactamase activity is present in two different superfamilies: the metallo-β-lactamase and the serine β-lactamase. The mechanism used to hydrolyze the β-lactam is different for the two superfamilies. We named this kind of evolution an allo-convergent evolution. We further showed that the β-lactamase activity evolved several times within each superfamily, a convergent evolution type that we named iso-convergent evolution. Both types of convergent evolution can be explained by the two evolutionary mechanisms discussed above. The probability of moving from one state to another is explained by the promiscuous β-lactamase activity present in the ancestral sequences of each superfamily, while the probability of fixation is explained in part by positive selection, as the organisms having β-lactamase activity allows them to resist organisms that secrete β-lactams. Indeed, an organism that has a mutation that increases the β-lactamase activity will be selected, as the organisms having this activity will have an advantage over the others.

show abstract

Section: Enzyme Convergent Evolution Via Allo-convergent and Iso-cmentioning

confidence: 99%

Section: Introduction: the Concepts: Iso And Allo-convergent Evolumentioning

confidence: 99%

Promiscuous Enzyme Activity as a Driver of Allo and Iso Convergent Evolution, Lessons from the β-Lactamases

Keshri

Chabrière

Pinault

et al. 2020

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…However, although the importance of soft tissue analysis in fossils is clearly recognised today 5 – 7 , investigations on soft tissue in the vertebral column, namely of joints and intervertebral spaces, have not been done 5 . Neither has the evolution of the intervertebral joint been reconstructed using phylogenetic methods such as ancestral state reconstruction (ASR) 8 .…”

Section: Introductionmentioning

confidence: 99%

Palaeontological evidence reveals convergent evolution of intervertebral joint types in amniotes

Scaal

Schellhorn

Kogan

et al. 2020

Sci Rep

View full text Add to dashboard Cite

the intervertebral disc (iVD) has long been considered unique to mammals. palaeohistological sampling of 17 mostly extinct clades across the amniote tree revealed preservation of different intervertebral soft tissue types (cartilage, probable notochord) seen in extant reptiles. The distribution of the fossilised tissues allowed us to infer the soft part anatomy of the joint. Surprisingly, we also found evidence for an IVD in fossil reptiles, including non-avian dinosaurs, ichthyosaurs, plesiosaurs, and marine crocodiles. Based on the fossil dataset, we traced the evolution of the amniote intervertebral joint through ancestral character state reconstruction. The IVD evolved at least twice, in mammals and in extinct diapsid reptiles. From this reptilian IVD, extant reptile groups and some non-avian dinosaurs independently evolved a synovial ball-and-socket joint. The unique birds dorsal intervertebral joint evolved from this dinosaur joint. The tuatara and some geckos reverted to the ancestral persisting notochord. Morphology of the vertebral column has provided zoologists with key anatomical characters for groups of amniotes 1. This includes the intervertebral disc (IVD), a soft tissue feature, which has been considered to be unique to mammals 2-4. However, although the importance of soft tissue analysis in fossils is clearly recognised today 5-7 , investigations on soft tissue in the vertebral column, namely of joints and intervertebral spaces, have not been done 5. Neither has the evolution of the intervertebral joint been reconstructed using phylogenetic methods such as ancestral state reconstruction (ASR) 8. The intervertebral disc (IVD) is a fibrocartilaginous synarthrotic joint connecting the vertebral centra of mammals. It provides intervertebral flexibility, allowing for a wide range of movements and is involved in shock absorbance and transmission of mechanical forces 9,10. The IVD is thus of eminent biomechanical and clinical importance in the human vertebral column and has been studied from multiple perspectives in biological, medical and veterinary science 11-13. The crucial function of the IVD is to withstand forces acting on the axial skeleton, and gradual failure of IVD function from degenerative processes often leads to pathological symptoms 14. The mammalian IVD is composed of two distinct parts, the nucleus pulposus (NP) and the annulus fibrosus (AF). The NP is the hydrophilic proteoglycan-rich gelatinous core of the IVD. Surrounding the NP is the AF, a lamellate ring of spirally arranged layers of collagen I and fibrocartilage. The joint formed by the IVD is further stabilized by intervertebral ligaments that insert in the periosteal cortex of the adjacent vertebral centra. Due to the lack of soft tissue preservation in fossils, however, the evolutionary origins of the IVD among Amniota (true land animals) have been poorly understood 10. As increasing numbers of fossil amniote specimens

show abstract

“…Evolutionary convergence, which is part of what is called homoplasy in cladistics, is a key concept in evolutionary biology (Pontarotti & Hue, ; Stayton, ). It is indeed an important and rather common evolutionary phenomenom, which may involve all kinds of traits, including behavioural, morphological, developmental, and molecular ones.…”

Section: Introductionmentioning

confidence: 99%

Detecting the molecular basis of phenotypic convergence

et al. 2018

Self Cite

View full text Add to dashboard Cite

Convergence is the process by which several species independently develop similar traits. This evolutionary process is not only strongly related to fundamental questions such as the predictability of evolution and the role of adaptation, its study also may provide new insights about genes involved in the convergent phenotype. We focus on this latter question and aim to detect the molecular basis of a given phenotypic convergence. After pointing out a number of concerns with current detection methods based on ancestral reconstruction, we propose a novel approach combining an original measure, called convergence index, which associates to any proteic site a quantity reflecting the extent to which it supports a phenotypic convergence, with a statistical framework for selecting genes from the convergence indices of all their sites. First, our measure of the “convergence level” outperforms two previous ones in distinguishing simulated convergent sites from nonconvergent ones. Second, by applying our detection approach to the well‐studied case of convergent echolocation between dolphins and bats, we identified a set of genes which is very significantly annotated with audition‐related GO terms. This result constitutes an indirect evidence that genes involved in a phenotypic convergence can be identified with a genome‐wide approach, a point which was highly debated, notably in the echolocation case. Our approach paves the way to systematic studies of numerous examples of convergent evolution in order to link convergent phenotypes to genotypes.

show abstract

Road Map to Study Convergent Evolution: A Proposition for Evolutionary Systems Biology Approaches

Cited by 12 publications

References 56 publications

Promiscuous Enzyme Activity as a Driver of Allo and Iso Convergent Evolution, Lessons from the β-Lactamases

Promiscuous Enzyme Activity as a Driver of Allo and Iso Convergent Evolution, Lessons from the β-Lactamases

Palaeontological evidence reveals convergent evolution of intervertebral joint types in amniotes

Detecting the molecular basis of phenotypic convergence

Contact Info

Product

Resources

About