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PubMed2005

Convergence and the multidimensional niche.

Convergent evolution has played an important role in the development of the ecological niche concept. We investigated patterns of convergent and divergent evolution of Caribbean Anolis lizards. These lizards diversified independently on each of the islands of the Greater Antilles, producing the same set of habitat specialists on each island. Using a phylogenetic comparative framework, we examined patterns of morphological convergence in five functionally distinct sets of morphological characters: body size, body shape, head shape, lamella number, and sexual size dimorphism. We find evidence for convergence among members of the habitat specialist types for each of these five datasets. Furthermore, the patterns of convergence differ among at least four of the five datasets; habitat specialists that are similar for one set of characters are often greatly different for another. This suggests that the habitat specialist niches into which these anoles have evolved are multidimensional, involving several distinct and independent aspects of morphology.

Adaptation, Biological↗
PubMed1994

alpha/beta barrel evolution and the modular assembly of enzymes: emerging trends in the flavin oxidase/dehydrogenase family.

Alpha/beta barrels have an ill-defined origin. Evidence exists which favours their divergent evolution from a common ancestral barrel and convergent evolution to a stable fold. However, recent sequence and structural information for the flavin oxidase/dehydrogenase family of barrel enzymes indicate that sub-families of alpha/beta barrels have evolved divergently. The modular fusion of barrel domains with core structures from other gene families has also contributed to the evolution of related but catalytically distinct enzyme molecules within each sub-family of the flavin oxidases/dehydrogenases. An analysis of the structures and sequences of the flavin oxidases/dehydrogenases has now enabled studies focusing on the evolutionary origins and modular assembly of this important family of proteins to be initiated.

Amino Acid Sequence↗
PubMed2000

Language trees support the express-train sequence of Austronesian expansion.

Languages, like molecules, document evolutionary history. Darwin observed that evolutionary change in languages greatly resembled the processes of biological evolution: inheritance from a common ancestor and convergent evolution operate in both. Despite many suggestions, few attempts have been made to apply the phylogenetic methods used in biology to linguistic data. Here we report a parsimony analysis of a large language data set. We use this analysis to test competing hypotheses--the "express-train" and the "entangled-bank" models--for the colonization of the Pacific by Austronesian-speaking peoples. The parsimony analysis of a matrix of 77 Austronesian languages with 5,185 lexical items produced a single most-parsimonious tree. The express-train model was converted into an ordered geographical character and mapped onto the language tree. We found that the topology of the language tree was highly compatible with the express-train model.

Archaeology↗
PubMed2005

A chimeric photoreceptor gene, NEOCHROME, has arisen twice during plant evolution.

Although most plant species from algae to flowering plants use blue light for inducing phototropism and chloroplast movement, many ferns, some mosses, and green algae use red as well as blue light for the regulation of these responses, resulting in better sensitivity at low light levels. During their evolution, ferns have created a chimeric photoreceptor (phy3 in Adiantum) between phytochrome (phy) and phototropin (phot) enabling them to use red light effectively. We have identified two genes resembling Adiantum PHY3, NEOCHROME1 and NEOCHROME2 (MsNEO1 and MsNEO2), in the green alga Mougeotia scalaris, a plant famous for its light-regulated chloroplast movement. Like Adiantum PHY3, both MsNEO gene products show phytochrome-typical bilin binding and red/far-red reversibility, the difference spectra matching the known action spectra of light-induced chloroplast movement in Mougeotia. Furthermore, both genes rescue red-light-induced chloroplast movement in Adiantum phy3 mutants, indicating functional equivalence. However, the fern and algal genes seem to have arisen independently in evolution, thus providing an intriguing example of convergent evolution.

Adiantum↗
PubMed1973

Relatedness among contractile and membrane proteins: evidence for evolution from common ancestral genes.

A statistical method for quantifying the relatedness among proteins was used to perform 2926 paired comparisons of amino-acid composition among 77 contractile and membrane-associated proteins from diverse species and sources. Relatedness of amino-acid compositions correlates with homology of amino-acid sequence. A high degree of relatedness was detected among K(+)-dependent membrane ATPase of Streptococcus faecalis, coupling factors F(1) and CF(1) from mitochondria and chloroplasts, outer fiber protein of cilia, ciliary dynein, tubulin, various actins, and myosin subfragment S-1. Heavy meromyosin and tropomyosin were related to each other but not to the first group of proteins. Differences in the degree of methylation may account for some differences in physiological function. Because of their diverse sources, the high degree of relatedness among these proteins is more compatible with evolution from common ancestral genes than with convergent evolution. Squid axon filarin, molluscan paramyosin, and bacterial flagellins appear to be unrelated either to each other or to any of the other proteins studied. Existence of persistent homologies among so many diverse proteins implies conservation of genetic information during evolution by utilization of codons for preferred amino-acid sequences in various proteins.

Actins↗
PubMed2003

Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism.

Cases of convergent evolution that involve changes in the same developmental pathway, called parallelism, provide evidence that a limited number of developmental changes are available to evolve a particular phenotype. To our knowledge, in no case are the genetic changes underlying morphological convergence understood. However, morphological convergence is not generally assumed to imply developmental parallelism. Here we investigate a case of convergence of larval morphology in insects and show that the loss of particular trichomes, observed in one species of the Drosophila melanogaster species group, has independently evolved multiple times in the distantly related D. virilis species group. We present genetic and gene expression data showing that regulatory changes of the shavenbaby/ovo (svb/ovo) gene underlie all independent cases of this morphological convergence. Our results indicate that some developmental regulators might preferentially accumulate evolutionary changes and that morphological parallelism might therefore be more common than previously appreciated.

Animals↗
PubMed2003

Who came first--larvae or adults? origins of bilaterian metazoan larvae.

There is a classic controversy in zoology over whether the common ancestor of living bilaterian phyla was a benthic animal with a bilaterian body plan, or was a pelagic larva-like animal similar to what we see today in the primary larvae of indirect-developing bilaterians. We examine the current larva-like adult hypothesis, and present an alternate model for the evolution of complex life histories by intercalation of larval features into the ontogeny of an ancestral direct-developing bilaterian. This gradual accumulation of larval features results in a developmental regulatory program that produces a larva distinct in body plan from the adult. The evolution of a rapid and complete metamorphosis is made possible by the convergent evolution of set aside cells in the final stages of the emergence of indirect developing larval forms. Although convergences abound either hypothesis for the evolution of developmental pathways and life histories, the bilaterian first hypothesis is consistent with all stages of evolution of a complex life history being selectively advantageous, with the rapid evolution of larval forms, and with the frequent co-option of genes from the adult phase of the life cycle prevalent in the evolution of embryos and larvae.

Animals↗
PubMed2026

Global lessons from antibiotic resistance: Metformin-hydrolysing genes in transposable elements, a new threat for type II diabetic patients?

OBJECTIVES: To investigate the evolutionary origin, genomic mobility, and potential dissemination of metformin-hydrolysing genes (mfmAB), and to assess whether environmental selection by metformin pollution may drive the emergence of transferable pharmaceutical-degrading traits analogous to antibiotic resistance. METHODS: Large-scale comparative genomics was performed using publicly available bacterial genomes carrying mfmAB homologs. Phylogenomic reconstruction, average nucleotide identity analysis, genomic context comparison, plasmid characterization, and insertion sequence mapping were used to infer evolutionary history and identify mechanisms of horizontal gene transfer. RESULTS: mfmAB homologs were identified in twelve Aminobacter and three Pseudomonas genomes within a conserved ∼8.2 kb gene cluster. Phylogenomic analyses showed that metformin-degrading capacity emerged independently in multiple Aminobacter lineages across distinct continents, consistent with convergent evolution under anthropogenic selective pressure. Genomic comparisons indicated a chromosomal origin of mfmAB, followed by mobilization onto conjugative plasmids through IS1182-mediated transposition. In Pseudomonas, additional IS3/IS6-mediated transposition events integrated mfmAB into diverse plasmid backbones, frequently within composite transposons also encoding guanylurea and biguanide degradation pathways (guuH, bguH). These findings reveal a dynamic modular assembly of metabolic functions facilitating adaptation to pharmaceutical pollutants. CONCLUSIONS: Metformin pollution appears to promote the emergence and mobilization of pharmaceutical-degrading genes through mechanisms paralleling antibiotic resistance evolution. Although no clinical impact has yet been demonstrated, the potential spread of such genes into human-associated microbiomes and their possible co-selection with antibiotic resistance determinants represent an emerging One Health concern. Environmental surveillance of pharmaceutical-degrading genes is warranted to anticipate future threats to drug efficacy.

Convergent evolution↗
PubMed2003

Phylogenetic signal in the song of crests and kinglets (Aves: Regulus).

Territorial song structures are often the most prominent characters for distinguishing closely related taxa among songbirds. Learning processes may cause convergent evolution of passerine songs, but phylogenetic information of acoustic traits can be investigated with the help of molecular phylogenies, which are not affected by cultural evolutionary processes. We used a phylogeny based on cytochrome b sequences to trace the evolution of territorial song within the genus Regulus. Five discrete song units are defined as basic components of regulid song via sonagraphic measurements. Traits of each unit are traced on a molecular tree and a mean acoustic character difference between taxon pairs is calculated. Acoustic divergence between regulid taxa correlates strongly with genetic distances. Syntax features of complete songs and of single units are most consistent with the molecular data, whereas the abundance of certain element types is not. Whether song characters are innate or learned was interpreted using hand-reared birds in aviary experiments. We found that convergent character evolution seems to be most probable for learned acoustic traits. We conclude that syntax traits of whole verses or subunits of territorial song, especially innate song structures, are the most reliable acoustic traits for phylogenetic reconstructions in Regulus.

Animals↗
PubMed2026

A Comprehensive Review on the Biosynthesis of Tropane Alkaloids.

Tropane alkaloids (TA) constitute a class of plant specialized metabolites with important pharmaceutical applications, including the anticholinergic agents hyoscyamine and scopolamine and the local anesthetic cocaine. Over the past decade, advances in genomics, structural biology, and synthetic biology have substantially revised our understanding of TA biosynthesis, leading to the identification of numerous key biosynthetic enzymes and evolutionary mechanisms. This review comprehensively summarizes current knowledge of TA biosynthesis from precursor formation to structurally diverse end products. We describe the pathway from putrescine to tropinone, the stereoselective metabolic branching mediated by Tropinone Reductases, and the downstream biosynthesis of medicinal tropane alkaloids, calystegines, and cocaine. Particular emphasis is placed on recent discoveries concerning catalytic mechanisms, structural determinants of substrate specificity, metabolic compartmentalization, and the convergent evolution of TA biosynthesis in Solanaceae and Erythroxylaceae. We further integrate advances in genomics, evolutionary biology, and metabolic engineering to highlight emerging strategies for microbial production and pathway redesign. By providing a comprehensive synthesis of recent progress and critical perspectives on unresolved questions, this review offers an updated framework for understanding TA biosynthesis and supports future research in plant specialized metabolism, synthetic biology, and natural product engineering.

Tropanes↗
PubMed2004

Chloroplast DNA inheritance and variation in Leucadendron species (Proteaceae) as revealed by PCR-RFLP.

The inheritance of chloroplast DNA (cpDNA) in Leucadendron species was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. A total of 100 progeny from five interspecific crosses involving seven parental species were tested, and all progeny exhibited the cpDNA restriction fragment pattern of the female parent, indicating that cpDNA in Leucadendron is maternally inherited. PCR-RFLP was also employed to study cpDNA variation among 21 Leucadendron species. Parsimony analysis using a heuristic search resulted in a phylogenetic tree that showed limited agreement to the taxonomic classification of Leucadendron species, based on morphological characteristics. The incongruence between cpDNA phylogenetic and taxonomic groupings in Leucadendron may be due to reticulate evolution involving a combination of hybridization and introgression, convergent evolution and/or lineage sorting at the interspecific, intersubsectional and intersectional levels.

Crosses, Genetic↗
PubMed1982

Somatic cell parasitism and the evolution of somatic tissue compatibility.

Selection pressures proposed to account for the convergent evolution of self/not-self recognition systems in lower organisms include defense against microbial parasites and somatic cell variants. Direct support for the existence of somatic cell parasites in natural populations has been lacking. I here report the occurrence of a somatic cell parasite in the cellular slime mold Dictyostelium mucoroides and discuss the implications of this phenomenon to the evolution of mechanisms of somatic tissue compatibility.

Animals↗
PubMed1997

Detection of convergent and parallel evolution at the amino acid sequence level.

Adaptive evolution at the molecular level can be studied by detecting convergent and parallel evolution at the amino acid sequence level. For a set of homologous protein sequences, the ancestral amino acids at all interior nodes of the phylogenetic tree of the proteins can be statistically inferred. The amino acid sites that have experienced convergent or parallel changes on independent evolutionary lineages can then be identified by comparing the amino acids at the beginning and end of each lineage. At present, the efficiency of the methods of ancestral sequence inference in identifying convergent and parallel changes is unknown. More seriously, when we identify convergent or parallel changes, it is unclear whether these changes are attributable to random chance. For these reasons, claims of convergent and parallel evolution at the amino acid sequence level have been disputed. We have conducted computer simulations to assess the efficiencies, of the parsimony and Bayesian methods of ancestral sequence inference in identifying convergent and parallel-change sites. Our results showed that the Bayesian method performs better than the parsimony method in identifying parallel changes, and both methods are inefficient in identifying convergent changes. However, the Bayesian method is recommended for estimating the number of convergent-change sites because it gives a conservative estimate. We have developed statistical tests for examining whether the observed numbers of convergent and parallel changes are due to random chance. As an example, we reanalyzed the stomach lysozyme sequences of foregut fermenters and found that parallel evolution is statistically significant, whereas convergent evolution is not well supported.

Amino Acid Sequence↗
PubMed1991

Evolutionary trends of neurofilament proteins in fish.

1. Neurofilament complement was studied in an early chordate (Ciona intestinalis) and six fish species by immunoblot with antisera specific for each of the three mammalian NF subunits. 2. The anti-NF-H and anti-NF-M antisera were characterized as strictly specific for phosphorylated epitopes located in the carboxyterminal domain. 3. The NF-L subunit is absent in primitive chordates and appears first in fish; it can be identified on the basis of its apparent mol. wt, its reactivity with the anti-IFA antibody and with polyclonal antibodies raised to the NF-L subunit of mammals. 4. Primitive chordate neurofilaments are constituted by a single polypeptide of ca 160,000 mol. wt exhibiting only M-type phosphorylation-dependent epitopes. 5. Primitive fish (Acipenser transmontanus, Salmo gairdneri, Scorpaena porcus, Serranus scriba) possess only a single high mol. wt NF subunit reacting with both anti-NF-H and anti-NF-M antiserum while more recent species (Mugil saliens, Perca fluviatilis) possess two high mol. wt NF subunits which are immunologically distinct as to their phosphorylation structures. 6. The existence in some fish species of two high mol. wt NF polypeptides suggests that the process of gene duplication and diversification supposed to have given rise to the two high mol. wt NF subunits of mammals and birds has occurred repeatedly in vertebrate evolution, and may be regarded as a case of convergent evolution.

Amino Acid Sequence↗
PubMed2004

Evolution of cyanobacterial and plant phytochromes.

Phytochromes are broadly distributed photochromic photoreceptors that are most sensitive in the red and far-red region of the visible spectrum. Three different bilins can be used as chromophores: plant phytochromes incorporate phytochromobilin, while phycocyanobilin serves as a chromophore of some cyanobacterial phytochromes, whereas all other phytochromes, including cyanobacterial orthologs incorporate biliverdin. During the evolution of plant and cyanobacterial phytochromes, the chromophore binding site has changed from a cysteine close to the N-terminus of the protein, the biliverdin attachment site, to a cysteine which lies within the so-called GAF domain and serves as phytochromobilin or phycocyanobilin attachment site. Since phylogenetic analyses imply that plant phytochromes are not direct successors of cyanobacterial phytochromes, chromophore exchange and the switch of the chromophore binding site has probably occurred at least twice in evolution. This may be regarded as an example for convergent evolution at the molecular level.

Cyanobacteria↗
PubMed1991

Is the guinea-pig a rodent?

The guinea-pig (Cavia porcellus), traditionally classified as a New World hystricomorph rodent, often shows anomalous morphological and molecular features in comparison with other eutherian mammals. For example, its insulin differs from that of other mammals in anabolic and growth-promoting activities and in its capability to form hexamers. Indeed, the literature about the molecular evolution of guinea-pigs abounds in references to 'convergent evolution', 'extremely rapid rates of substitution', and 'unique evolutionary mechanisms'. These claims are based on the assumption that the guinea-pig is a rodent. Our phylogenetic analyses of amino-acid sequence data, however, imply that the guinea-pig diverged before the separation of the primates and the artiodactyls from the myomorph rodents (rats and mice). If true, then the myomorphs and the caviomorphs do not constitute a natural clade, and the Caviomorpha (or the Histricomorpha) should be elevated in taxonomical rank and regarded as a separate mammalian order distinct from the Rodentia. If, as suggested by recent data, the myomorphs branched off before the divergence among the carnivores, lagomorphs, artiodactyls and primates, then the new order would represent an early divergence in eutherian radiation.

Animals↗
PubMed2025

Global Environmental Factors Impact the Evolution of Adult Hemoglobins in Squamata Reptiles (Lizards and Snakes) and Terrestrial Turtles.

Convergent evolution of oxygen transport mechanisms arises from respiratory proteins adapting to similar environmental pressures. We examined this relationship between adult hemoglobin subunits (Hbs: HBA1, HBAD, HBB1, and HBB2) found in land reptiles (lizards, snakes, and turtles) with their global distribution variables: Altitude, latitude, ambient temperature, and biomass production. We found that biomass was positively associated with the synonymous substitution rate (dS) of HBAD, while it showed the opposite trend for HBB2 in snakes. Additionally, latitude was negatively related to the dS of HBB2 in snakes, but nonsignificant with other Hbs. Altitude was negatively associated with ω = dN/dS of HBA1 and HBAD, whereas temperature showed a similar negative trend with the ω of HBAD across reptiles and in HBB2 of snakes. At amino acid sites, we found most were conserved except for 11 (two near the heme-binding pocket) across Hbs. These fast-changing sites shifted from polar to nonpolar residues, showing a pattern seen in high-altitude mammals. Our results highlight that in reptiles (i) Hbs are diversifying at individual amino acid sites while generally some subunits exhibiting lower ω rates at higher altitudes and hotter temperatures, with the later and higher biomass ecosystems also linked to increases in dS; (ii) HBBs are the most conserved of the Hbs; (iii) latitudinal gradients only show a significant association with the dS of HBB2 in snakes; and (iv) gene conversion events occurred across HBBs in reptiles, which confound their homology assignation, except for snakes that evidenced a single major duplication in their HBBs.

Animals↗
PubMed1997

Comparative anatomy of the aldo-keto reductase superfamily.

The aldo-keto reductases metabolize a wide range of substrates and are potential drug targets. This protein superfamily includes aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases and dihydrodiol dehydrogenases. By combining multiple sequence alignments with known three-dimensional structures and the results of site-directed mutagenesis studies, we have developed a structure/function analysis of this superfamily. Our studies suggest that the (alpha/beta)8-barrel fold provides a common scaffold for an NAD(P)(H)-dependent catalytic activity, with substrate specificity determined by variation of loops on the C-terminal side of the barrel. All the aldo-keto reductases are dependent on nicotinamide cofactors for catalysis and retain a similar cofactor binding site, even among proteins with less than 30% amino acid sequence identity. Likewise, the aldo-keto reductase active site is highly conserved. However, our alignments indicate that variation ofa single residue in the active site may alter the reaction mechanism from carbonyl oxidoreduction to carbon-carbon double-bond reduction, as in the 3-oxo-5beta-steroid 4-dehydrogenases (Delta4-3-ketosteroid 5beta-reductases) of the superfamily. Comparison of the proposed substrate binding pocket suggests residues 54 and 118, near the active site, as possible discriminators between sugar and steroid substrates. In addition, sequence alignment and subsequent homology modelling of mouse liver 17beta-hydroxysteroid dehydrogenase and rat ovary 20alpha-hydroxysteroid dehydrogenase indicate that three loops on the C-terminal side of the barrel play potential roles in determining the positional and stereo-specificity of the hydroxysteroid dehydrogenases. Finally, we propose that the aldo-keto reductase superfamily may represent an example of divergent evolution from an ancestral multifunctional oxidoreductase and an example of convergent evolution to the same active-site constellation as the short-chain dehydrogenase/reductase superfamily.

Alcohol Oxidoreductases↗