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PubMed1994

The evolution and structure of aminergic G protein-coupled receptors.

An analysis of aligned sequences of the seven transmembrane segments of 59 aminergic G protein-coupled receptors (GPCRs) shows that their classification into subclasses based upon the nature of their ligands is over-simplified. Sequences similarity dendrograms indicate that the evolution of these receptors occurs at two sites (the G protein-coupling regions and the ligand binding site) and this results in convergent as well as divergent evolution. Amino acid substitution patterns at each position in the alignment discriminate between the internal residues and those that face the lipid and the periodicity in these patterns matches that of the classical alpha-helix. The point at which the fifth transmembrane helix protrudes into the cytoplasm and the point at which the seventh transmembrane helix protrudes on the extracellular side of the bilayer are detected. The positions of charged residues on the external face of the remaining helices are used to determine the point at which they enter and leave the bilayer. These data are used to construct three-dimensional models of GPCRs, which are based on the recently determined arrangement of the helices of bovine rhodopsin rather than on the structure of bacteriorhodopsin.

Amino Acid Sequence↗

PubMed2003

Genetic mechanisms and constraints governing the evolution of correlated traits in drosophilid flies.

Some morphological traits differ greatly between related species, but it is not clear whether diversity evolves through changes in the same genes and whether similar, independent (that is, convergent) changes occur by the same mechanism. Pigmentation in fruitflies presents an attractive opportunity to explore these issues because pigmentation patterns are diverse, similar patterns have arisen in independent clades, and numerous genes governing their formation have been identified in Drosophila melanogaster. Here we show that both evolutionary diversification and convergence can be due to evolution at the same locus, by comparing abdominal pigmentation and trichome patterns and the expression of Bric-à-brac2 (Bab2), which regulates both traits in D. melanogaster, in 13 species representing the major clades of the subfamily Drosophilinae. Modifications of Bab2 expression are frequently correlated with diverse pigmentation and trichome patterns that evolved independently in multiple lineages. In a few species, Bab2 expression is not correlated with changes in pigmentation but is correlated with a conserved pattern of trichomes, indicating that this locus can be circumvented to evolve new patterns when a correlated trait is under different constraints.

Animals↗

PubMed1996

Unusual evolution of 11beta- and 17beta-hydroxysteroid and retinol dehydrogenases.

11beta-hydroxysteroid dehydrogenases regulate glucocorticoid concentrations and 17beta-hydroxysteroid dehydrogenases regulate estrogen and androgen concentrations in mammals. Phylogenetic analysis of the sequences from two 11beta-hydroxysteroid dehydrogenases and four mammalian 17beta-hydroxysteroid dehydrogenases indicates unusual evolution in these enzymes. Type 1 11beta- and 17beta-hydroxysteroid dehydrogenases are on the same branch; Type 2 enzymes cluster on another branch with beta-hydroxybutyrate dehydrogenase,11-cis-retinol dehydrogenase and retinol dehydrogenase; Type 3 17beta-hydroxysteroid dehydrogenase is on a third branch; while the pig dehydrogenase clusters with a yeast multifunctional enzyme on a fourth branch. Pig 17beta-hydroxysteroid dehydrogenase appears to have evolved independently from the other three 17beta-hydroxysteroid dehydrogenases; in which case, the evolution of 17beta-hydroxysteroid dehydrogenase activity is an example of functional convergence. The phylogeny also suggests that independent evolution of specificity toward C11 substituents on glucocorticoids and C17 substituents on androgens and estrogens has occurred in Types 1 and 2 11beta- and 17beta-hydroxysteroid dehydrogenases.

11-beta-Hydroxysteroid Dehydrogenases↗

PubMed2005

Correlated evolution of maternally derived yolk testosterone and early developmental traits in passerine birds.

Recent studies on hormone-mediated maternal effects in birds have highlighted the influence of variable maternal yolk androgen concentration on offspring phenotype, particularly in terms of early development. If genetic differences between laying females regulate variation in yolk hormone concentration, then this physiological maternal effect is an indirect genetic effect which can provide a basis for the co-evolution of maternal and offspring phenotypes. Thus, we investigated the evolutionary associations between maternally derived yolk testosterone (T) and early developmental traits in passerine birds via a comparative, phylogenetic analysis. Our results from species-correlation and independent contrasts analyses provide convergent evidence for the correlated evolution of maternal yolk T concentration and length of the prenatal developmental period in passerines. Here, we show these traits are significantly negatively associated (species-correlation: p<0.001, r2=0.85; independent contrasts: p=0.005). Our results highlight the need for more studies investigating the role of yolk hormones in evolutionary processes concerning maternal effects.

Animals↗

PubMed2002

[Conditionally neutral phylogenetic markers of major taxa: a new aspect of the evolution of macromolecules].

The current phase of molecular phylogenetics can be named the 18S rRNA gene era, which is now approaching the end. To date, almost all phyla of metazoans and many taxa of protists are represented in databases of 18S rRNA gene sequences. The elements of the phylogenetic tree of Metazoa inferred from 18S rRNA genes are characterized by unequal validity: some of them seem to be well grounded; others are not adequately supported, and probably will be revised later. The validity of phylogenetic reconstruction is influenced by two main factors: (1) erroneous grouping of long branches that occur because of abnormally high evolution rate; (2) deficit of phylogenetically informative characters. A method for overcoming these difficulties is suggested in addition to known tools: using phylogenetic markers that are stable within individual taxa and evolve by punctuated equilibrium. These markers are least influenced by the convergence caused by a high evolution rate of the entire gene. The nature of these markers of ancient taxa, paradoxical from the perspective of neutral evolution, is discussed, as well as their importance for establishing monophyly of both new large-scale taxonomic groups of invertebrates (Bilateria + Rhombozoa + Orthonectida + Myxozoa + Cnidaria + Placozoa and Echinodermata + Hemichordata) and some major taxa of Nematoda.

Animals↗

PubMed2026

Back on the ground: genome analysis of convergent flight loss in rails.

Similar phenotypic traits can evolve independently in response to comparable environmental challenges. A striking example of this process is the repeated and irreversible loss of flight in birds, particularly on islands. The rail family (Rallidae) provides an exceptional model for studying this phenomenon, as nearly a quarter of the 130 extant species have independently become flightless. Here, we present the first genome-wide comparative analysis of multiple independent flightless rail lineages to identify the molecular basis of flight loss. We compared coding regions from 7 rail species (4 flightless and 3 volant) using more than 11,000 alignments and multiple phylogeny-based tests, including branch-site models of selection, relative evolutionary rate analyses, and assessments of function-altering amino acid substitutions. Across all analyses, 116 genes showed significant associations with flightlessness, of which 37 were linked to biological functions related to flight capacity-such as muscle, bone, limb, and heart development-or to traits reflecting ecological consequences of flight loss, including immune response, renal function, lipid metabolism, cognition, and sensory perception. Many genes under selection in flightless species were also involved in gene regulation and post-translational modification. These findings suggest that convergent loss of flight in rails arises not from major mutations in a few key loci but from numerous small, repeated genetic changes affecting both developmental pathways and regulatory mechanisms.

Animals↗

PubMed2002

Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity.

Class 1 release factor in eukaryotes (eRF1) recognizes stop codons and promotes peptide release from the ribosome. The 'molecular mimicry' hypothesis suggests that domain 1 of eRF1 is analogous to the tRNA anticodon stem-loop. Recent studies strongly support this hypothesis and several models for specific interactions between stop codons and residues in domain 1 have been proposed. In this study we have sequenced and identified novel eRF1 sequences across a wide diversity of eukaryotes and re-evaluated the codon-binding site by bioinformatic analyses of a large eRF1 dataset. Analyses of the eRF1 structure combined with estimates of evolutionary rates at amino acid sites allow us to define the residues that are under structural (i.e. those involved in intramolecular interactions) versus non-structural selective constraints. Furthermore, we have re-assessed convergent substitutions in the ciliate variant code eRF1s using maximum likelihood-based phylogenetic approaches. Our results favor the model proposed by Bertram et al. that stop codons bind to three 'cavities' on the protein surface, although we suggest that the stop codon may bind in the opposite orientation to the original model. We assess the feasibility of this alternative binding orientation with a triplet stop codon and the eRF1 domain 1 structures using molecular modeling techniques.

Amino Acid Sequence↗

PubMed1995

The multiregional and single origin hypotheses of the evolution of modern man: a reconciliation.

A current debate opposes two theories of the origin of modern man. One view is that modern Homo sapiens emerged from Africa relatively recently, most probably within the last two or three hundred thousand years (Wilson & Cann, 1992, Sci. Am. 266(4), 22-27). The opposing view is that modern man has resulted from parallel evolution in different regions, producing convergent modernization of local populations over the last million years or so--the multiregional model (Frayer et al., 1993, Am. Anthrop. 95, 14-50). Proponents of both views believe that their interpretations are irreconcilable. The object of the present paper is to describe a genetic mechanism--mitochondrial exclusion--which offers a basis for a model of human evolution that is compatible with the evidence adduced for both contemporary views. The model proposes a mechanism by which complete replacement of archaic mitochondrial DNA may have occurred in a population produced by recent admixture of archaic and modern types of man.

Animals↗

PubMed1997

Determinants of primate social organization: comparative evidence and new insights from Malagasy lemurs.

The aim of this review is to summarize newly available information on lemur social systems, to contrast it with the social organization of other primates and to relate it to existing models of primate social evolution. Because of their evolutionary history, the primates of Madagascar constitute a natural experiment in social evolution. During millions of years of isolation, they converged with other primates only in the most fundamental way in the evolution of solitary, pair-living and group-living species, but deviate in several respects within these basic categories of social organization. Solitary lemurs remain poorly studied, but their social organization appears to be broadly similar to that of other solitary primates, even though the unexpected lack of sexual dimorphism may indicate that similar types of social organization can give rise to different mating systems. The determinants of a solitary lifestyle remain elusive. Pair-living lemurs show striking convergences with other monogamous primates in several behavioural traits, but also deviate in that the majority of species are at least partly nocturnal and do not exhibit direct paternal care of dependent young. Group-living lemurs have not evolved single-male groups, male-bonded and multi-level societies, and polyandrous groups may also be lacking. Female philopatry is common, but female bonds are generally weakly developed and eviction of females from natal groups is not unusual. Group-living lemurs also differ from anthropoids in that their groups have even adult sex ratios, smaller average size and may split up on a seasonal basis. Feeding competition, predation risk and reproductive competition can not fully explain these unusual aspects of lemur social organization. It has therefore been suggested that the social consequences of the risk of infanticide and of recent changes in activity may be ultimately responsible for these idiosyncracies of group-living lemurs, an explanation largely supported by the available evidence. Thus, social factors and fundamental life-history traits, in addition to ecological factors, contribute importantly to variation in social systems among lemurs, and possibly other primates. However, neither the diversity of lemur social systems, nor the evolutionary forces and mechanisms operating in these and other primates are yet fully understood.

Animals↗

PubMed2004

From The Cover: Binocularity and brain evolution in primates.

Primates are distinguished by frontally directed, highly convergent orbits, which are associated with stereoscopic vision. Although stereoscopic vision requires specialized neural mechanisms, its implications for brain evolution are unknown. Using phylogenetic comparative analysis, I show that evolutionary increases among primate taxa in the degree of orbital convergence correlate with expansion of visual brain structures and, as a consequence, with the overall size of the brain. This pattern is found across the whole primate order and is also repeated within each of the two major primate subtaxa. The visual expansion associated with increased binocularity is specific to the parvocellular visual pathway, consistent with recent evidence implicating this pathway in fine-grained stereopsis. The results support the hypothesis that brain size evolution in primates was associated with visual specialization.

Animals↗

PubMed1997

Adaptation Models of Anisotropic Bone.

A theoretical model and numerical methods were developed for testing different bone internal remodelling stimuli. The keystone of the study was the formulation of a stimulus based on the mechanical invariants of the stress tensor, which took into account bone non-homogeneity and anisotropy. A non-site specific remodelling rate equation was then used for the apparent density whereas anisotropy was fixed and evaluated from anatomic observations. An node-based semi-implicit algorithm with adaptive stepsize was implemented for solving the evolution equation. To preclude numerical artifacts (non-convergence, instability), a phase space description was proposed. As an illustration, the evolution of apparent density distribution surrounding the femoral stem after a Total Hip Replacement was simulated. Three stimuli were tested: the strain energy density stimulus, the octahedral shear stress stimulus, and an anisotropic plastic yield stress stimulus.

Journal Article↗

PubMed2025

Characterisation of a persistent SARS-CoV-2 infection lasting more than 750 days in a person living with HIV: a genomic analysis.

BACKGROUND: People who are immunocompromised can develop persistent SARS-CoV-2 infections. Several viral mutations accumulated during the course of such persistent infections have also been observed in prominent variants of concern (VOCs). Here, we characterise persistent infection and viral evolution of SARS-CoV-2 lasting more than 750 days in a person with advanced HIV-1 infection. METHODS: Between March, 2021, and July, 2022, eight clinical specimens were collected from a person living with HIV, neither receiving antiretroviral therapy nor virally suppressed, and presumed to have been initially infected with SARS-CoV-2 in mid-May, 2020. Viral RNA was extracted from each swab and an amplicon-based sequencing approach was used for genomic analysis of SARS-CoV-2. Variable sites were characterised at the consensus and subconsensus levels, and phylogenetic tools were applied to analyse viral evolution. Publicly available SARS-CoV-2 sequences from GenBank were leveraged to contextualise our sequenced samples and identify any potential evidence of transmission. FINDINGS: Genomes formed a monophyletic cluster in the B.1 lineage. 68 consensus and 67 subconsensus single nucleotide variants were observed over the course of infection. The intrahost clock rate remained similar to that of the interhost rate in contemporaneous community sequences (6·74 × 10-4 [95% credible interval 5·05 × 10-4 to 8·54 × 10-4] substitutions per site per year vs 6·11 × 10-4 [5·54 × 10-5 to 6·66 × 10-4]). Mutations grouped into two distinct subpopulations present throughout infection. 10 non-synonymous mutations in the spike protein gene were at positions in common with those defining the omicron lineage (BA.1 or BA.2), of which nine were present before November, 2021. Nine of 18 substitutions present throughout infection were rare in online databases, suggesting a lack of long transmission chains descending from this individual. INTERPRETATION: Convergent SARS-CoV-2 evolution, both in and outside the spike protein, observed in this study suggests parallels with the evolutionary process leading to emergence of the omicron VOC. The inferred absence of onward infections might indicate a loss of transmissibility during adaptation to a single host. Our results underscore the importance of appropriate treatment to cure persistent SARS-CoV-2 infections and monitoring them to understand how mutations contribute to viral adaptation. FUNDING: National Institute of General Medical Sciences of the National Institutes of Health, Centers for Disease Control and Prevention, the National Institute of Allergy and Infectious Diseases, MassCPR, and Morris Singer Foundation.

Humans↗

PubMed2001

Common history at the origin of the position-function correlation in transcriptional regulators in archaea and bacteria.

Regulatory proteins in Escherichia coli with a helix-turn-helix (HTH) DNA binding motif show a position-function correlation such that repressors have this motif predominantly at the N terminus, whereas activators have the motif at the C-terminus extreme. Using this initial collection we identified by sequence comparison the exhaustive set of transcriptional regulators in 17 bacterial and 6 archaeal genomes. This enlarged set shows the same position-function correlation. The main question we address is whether this correlation is the result of common origin in evolution or the result of convergence. Evidence is presented supporting a common history at the origin of this correlation. We show the existence of a supergroup of eight repressor protein families sharing a conserved extended sequence comprising the classic HTH. Two of these repressor families (MarR and AsnC) originated before the divergence of Archaea and Bacteria. They are proposed at the origin of HTH-bearing transcriptional regulators currently present in Bacteria. The group of LysR proteins, with the HTH also at the N terminus, offers a control to the argument, since it shows clearly distinctive structural, functional, and evolutionary properties. This group of activator proteins, suggested to have originated within the Bacteria, has an advantageous gene organization to facilitate its horizontal transfer-used to conquer some Archaea-as well as negative autoregulation convenient for homeostasis, all of which agrees with this being the largest family in Bacteria. These results suggest that if shuffling of motifs occurred in Bacteria, it occurred only early in the history of these proteins, as opposed to what is observed in eukaryotic regulators.

Archaea↗

PubMed1996

What can 18S rDNA do for bivalve phylogeny?

Molecular characteristics, especially 18S rDNA sequences, may be of great value for the study of bivalve evolution and its numerous morphological convergencies once the reliability of these data can be evaluated. The analysis of 11 published complete molluscan sequences and two new ones, Arca noae and Atrina pectinata, reveals considerable differences in relative substitution rates. The gastropod and eulamellibranch species have the fastest and Atrina species have the slowest rates. Two methods are used to assess the information contents of the dataset in addition to bootstrap analysis, spectral analysis, and the "pattern of resolved nodes" technique. Tree reconstructions by parsimony, neighbor-joining, and maximum-likelihood differ in regard to the position of the eulamellibranch family Mactridae and of Crassostrea. Although there is a signal for the monophyly of Bivalvia, Mactridae cluster with Gastropoda in most runs, rendering Bivalvia diphyletic. The position of Crassostrea was extremely variable, probably due to the high substitution rate of this species. Atrina roots deeper than Arca in all trees, although a corresponding signal in spectral analysis is absent. Phylogenetic signals among the three pectinid species are low but sufficient to resolve the branching pattern. The tree inferred from the 18S rDNA and from morphological data has Bivalvia monophyletic with a basal polytomy of Mactridae, Crassostrea, and the remaining Pteriomorphia, where Arca branches off before Atrina and the Pectinidae. Argopecten is sister group to the other two pectinids; 18S sequence data will have great impact on our understanding of bivalve phylogeny, but only when more sequences of similar substitution rates are available.

Animals↗

PubMedDate not supplied

[Hypothesis of possible evolution and functional specialization based on the recombination and transposition of elementary functional blocks].

A number of examples demonstrating that different cell and organ functions are being performed by a limited set of identical or similar functional blocks has been analysed. The latters are molecular or supramolecular structures fulfilling elementary functions. Functional evolution, functional and structural specializations, divergence, convergence and other processes have been considered as associated largely with the relationship, recombination and transposition of such elementary functional blocks, presumably, originated at the early stages of evolution.

Animals↗

PubMed2005

Foraging behaviour of the slender loris (Loris lydekkerianus lydekkerianus): implications for theories of primate origins.

Members of the Order Primates are characterised by a wide overlap of visual fields or optic convergence. It has been proposed that exploitation of either insects or angiosperm products in the terminal branches of trees, and the corresponding complex, three-dimensional environment associated with these foraging strategies, account for visual convergence. Although slender lorises (Loris sp.) are the most visually convergent of all the primates, very little is known about their feeding ecology. This study, carried out over 10 (1/2) months in South India, examines the feeding behaviour of L. lydekkerianus lydekkerianus in relation to hypotheses regarding visual predation of insects. Of 1238 feeding observations, 96% were of animal prey. Lorises showed an equal and overwhelming preference for terminal and middle branch feeding, using the undergrowth and trunk rarely. The type of prey caught on terminal branches (Lepidoptera, Odonata, Homoptera) differed significantly from those caught on middle branches (Hymenoptera, Coleoptera). A two-handed catch accompanied by bipedal postures was used almost exclusively on terminal branches where mobile prey was caught, whereas the more common capture technique of one-handed grab was used more often on sturdy middle branches to obtain slow moving prey. Although prey was detected with senses other than vision, vision was the key sense used upon the final strike. This study strongly supports the notion that hunting for animal prey was a key ecological determinant in selecting for visual convergence early on in primate evolution. The extreme specialisations of slender lorises, however, suggest that early primates were not dedicated faunivores and lend further support to the emerging view that both insects and fruits were probably important components of the diet of basal primates, and that exploitation of fruits may account for other key primate traits.

Animals↗

PubMed2002

Principles of structures of animal and plant lectins.

Lectins form a diverse group of protein families that have in common their ability to specifically recognize certain carbohydrates. Crystal structures of members of the different animal and plant lectin families have revealed a wide variety of lectin folds and carbohydrate binding site architectures. Despite this large variability, a number of interesting cases of convergent as well as divergent evolution among animal and plant lectin families can be noted. These similarities exist at the levels of the protein fold, the architecture of the binding site as well as quaternary structure and may be derived from similar functional needs.

Animals↗

PubMed1993

Habitat-dependent hybrid parentage and differential introgression between neighboringly sympatric Daphnia species.

Allozyme, morphological, and PCR-generated mtDNA markers were used to analyze hybrid parentage and introgression between the neighboringly sympatric crustaceans Daphnia galeata mendotae and Daphnia rosea. mtDNA analysis of D. galeata mendotae from 15 lakes and of D. rosea from 8 lakes revealed species-specific fragment patterns resulting from TaqI and RsaI digestion. No individuals of one parent species possessed the typical mtDNA of the other parent species, suggesting that mtDNA introgression is rare or nonexistent. Hybrids from 18 lakes possessed either the mtDNA patterns of D. rosea or of D. galeata mendotae, indicating that reciprocal hybridization occurs. The mtDNA genome of the dominant parent species in a lake was overrepresented in the hybrids, suggesting that hybridization most often involves females of the common species and males of the rare species. Such a pattern is consistent with the differing importance of density to the environmental induction of males and sexual eggs in Daphnia. For the assessment of nuclear gene flow, eight sympatric populations of each parental taxon and seven allopatric populations of D. galeata were analyzed for allozyme variation at nine polymorphic loci. Our results provided evidence for asymmetric interspecific gene flow involving alleles at six loci that are unlikely to be convergent or symplesiomorphic. This reticulate evolution accounted for much of the genetic divergence between European and North American populations of D. galeata.

Animals↗