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PubMed2006

Analysis of the mouse and human acyl-CoA thioesterase (ACOT) gene clusters shows that convergent, functional evolution results in a reduced number of human peroxisomal ACOTs.

The maintenance of cellular levels of free fatty acids and acyl-CoAs, the activated form of free fatty acids, is extremely important, as imbalances in lipid metabolism have serious consequences for human health. Acyl-coenzyme A (CoA) thioesterases (ACOTs) hydrolyze acyl-CoAs to the free fatty acid and CoASH, and thereby have the potential to regulate intracellular levels of these compounds. We previously identified and characterized a mouse ACOT gene cluster comprised of six genes that apparently arose by gene duplications encoding acyl-CoA thioesterases with localizations in cytosol (ACOT1), mitochondria (ACOT2), and peroxisomes (ACOT3-6). However, the corresponding human gene cluster contains only three genes (ACOT1, ACOT2, and ACOT4) coding for full-length thioesterase proteins, of which only one is peroxisomal (ACOT4). We therefore set out to characterize the human genes, and we show here that the human ACOT4 protein catalyzes the activities of three mouse peroxisomal ACOTs (ACOT3, 4, and 5), being active on succinyl-CoA and medium to long chain acyl-CoAs, while ACOT1 and ACOT2 carry out similar functions to the corresponding mouse genes. These data strongly suggest that the human ACOT4 gene has acquired the functions of three mouse genes by a functional convergent evolution that also provides an explanation for the unexpectedly low number of human genes.

Amino Acid Sequence↗
PubMed2002

A molecular phylogenetic study of the Palmae (Arecaceae) based on atpB, rbcL, and 18S nrDNA sequences.

Notoriously slow rates of molecular evolution and convergent evolution among some morphological characters have limited phylogenetic resolution for the palm family (Arecaceae). This study adds nuclear DNA (18S SSU rRNA) and chloroplast DNA (cpDNA; atpB and rbcL) sequence data for 65 genera of palms and characterizes molecular variation for each molecule. Phylogenetic relationships were estimated with maximum likelihood and maximum parsimony techniques for the new data and for previously published molecular data for 45 palm genera. Maximum parsimony analysis was also used to compare molecular and morphological data for 33 palm genera. Incongruence among datasets was detected between cpDNA and 18S data and between molecular and morphological data. Most conflict between nuclear and cpDNA data was associated with the genus Nypa. Several taxa showed relatively long branches with 18S data, but phylogenetic resolution of these taxa was essentially the same for 18S and cpDNA data. Base composition bias for 18S that contributed to erroneous phylogenetic resolution in other taxa did not seem to be present in Palmae. Morphological data were incongruent with all molecular data due to apparent morphological homoplasy for Caryoteae, Ceroxyloideae, Iriarteae, and Thrinacinae. Both cpDNA and nuclear 18S data firmly resolved Caryoteae with Borasseae of Coryphoideae, suggesting that at least some morphological characters used to place Caryoteae in Arecoideae are homoplastic. In this study, increased character sampling seems to be more important than increased taxon sampling; a comparison of the full (65-taxon) and reduced (45- and 33-taxon) datasets suggests little difference in core topology but considerably more nodal support with the increased character sample sizes. These results indicate a general trend toward a stable estimate of phylogenetic relationships for the Palmae. Although the 33-taxon topologies are even better resolved, they lack several critical taxa and are affected by incongruence between molecular and morphological data. As such, a comparison of results from the 45- and 33-taxon trees offers the best available reference for phylogenetic inference on palms.

Arecaceae↗
PubMed2006

Shared and unique features of diversification in Greater Antillean Anolis ecomorphs.

Examples of convergent evolution suggest that natural selection can often produce predictable evolutionary outcomes. However, unique histories among species can lead to divergent evolution regardless of their shared selective pressures-and some contend that such historical contingencies produce the dominant features of evolution. A classic example of convergent evolution is the set of Anolis lizard ecomorphs of the Greater Antilles. On each of four islands, anole species partition the structural habitat into at least four categories, exhibiting similar morphologies within each category. We assessed the relative importance of shared selection due to habitat similarity, unique island histories, and unique effects of similar habitats on different islands in the generation of morphological variation in anole ecomorphs. We found that shared features of diversification across habitats were of greatest importance, but island effects on morphology (reflecting either island effects per se or phylogenetic relationships) and unique aspects of habitat diversification on different islands were also important. There were three distinct cases of island-specific habitat diversification, and only one was confounded by phylogenetic relatedness. The other two unique aspects were not related to shared ancestry but might reflect as-yet-unmeasured environmental differences between islands in habitat characteristics. Quantifying the relative importance of shared and unique responses to similar selective regimes provides a more complete understanding of phenotypic diversification, even in this much-studied system.

Animals↗
PubMed2026

Functional convergence of regulatory regions provides vital insights into mammalian gliding adaptation.

Uncovering the key genetic basis of complex phenotypic convergence in distantly related species has been a long-standing focus in evolutionary biology and genetics, and the convergent evolution of gliding in mammals offers a valuable opportunity to address this question. Here, we investigated the genomic basis of convergent evolution of gliding in mammals by analyzing both protein-coding genes and conserved non-coding elements (CNEs). We first de novo assembled and annotated two chromosome-level genomes of gliding mammals, the red and white giant flying squirrel (Petaurista alborufus) and sugar gliders (Petaurus breviceps), and conducted comprehensive comparative genomic analysis combined with another gliding mammal, the Sunda flying lemur (Galeopterus variegatus) and 14 background species. We found that the convergent evolution of protein-coding genes provided relatively limited but functionally relevant evidence linked to gliding phenotypes. By contrast, we found that gliding-accelerated CNEs (GACNEs) cluster near functionally equivalent genes and frequently aggregate into highly diverged yet functionally convergent hotspot regions. Across the three gliding lineages, both GACNEs and hotspot GACNEs show strong convergence in their functional enrichment profiles, suggesting a broad genetic basis underlying the convergent gliding phenotype. Furthermore, we identified 72 core transcription factors underpinning the genetic basis of gliding convergence, including EMX2 and ZFHX3, potentially involved in multiple aspects of gliding adaptation. Our study highlights the role of functional convergence in regulatory regions as a key mechanism in mammalian gliding convergence, offering valuable insights and strategies for uncovering the genetic basis of complex convergent traits, thereby advancing understanding of the molecular basis of convergent traits.

Petaurista alborufus↗
PubMed2006

Nuclear markers reveal that inter-lake cichlids' similar morphologies do not reflect similar genealogy.

The apparent inter-lake morphological similarity among East African Great Lakes' cichlid species/genera has left evolutionary biologists asking whether such similarity is due to sharing of common ancestor or mere convergent evolution. In order to answer such question, we first used Geometric Morphometrics, GM, to quantify morphological similarity and then subsequently used Amplified Fragment Length Polymorphism, AFLP, to determine if similar morphologies imply shared ancestry or convergent evolution. GM revealed that not all presumed morphological similar pairs were indeed similar, and the dendrogram generated from AFLP data indicated distinct clusters corresponding to each lake and not inter-lake morphological similar pairs. Such results imply that the morphological similarity is due to convergent evolution and not shared ancestry. The congruency of GM and AFLP generated dendrograms imply that GM is capable of picking up phylogenetic signal, and thus GM can be potential tool in phylogenetic systematics.

Africa, Eastern↗
PubMed2006

An evolutionary perspective on caching by corvids.

A principal finding in the food-caching literature is that species differences in hoarding propensity are positively correlated with species differences in degree of adaptations to caching behaviour, such as performance on spatial memory tasks and hippocampal volume. However, there are examples that do not fit this pattern. We argue that these examples can be better understood by considering the phylogenetic relatedness between species. We reconstruct the ancestral state for caching behaviour in corvids and assess when transitions in caching behaviour occurred within the corvid phylogeny. Our analysis shows that the common ancestor of all corvids was a moderate cacher. This result suggests that corvids followed a bi-directional evolutionary trajectory in which caching was secondarily lost twice and there were at least two independent transitions from moderate to specialized caching. The independent evolution of specialized cachers in the two groups must, therefore, be a case of convergent evolution. This is exemplified by the fact that specialized cachers show structurally different adaptations serving the same function to intense caching, such as different pouches to transport food. Finally, we argue that convergent evolution may have led to adaptations in memory and hippocampus that serve the same function but differ in design, and that these different adaptations may explain the examples that do not fit the pattern predicted by the adaptive specialization hypothesis.

Animals↗
PubMed2025

The Pseudomonas aeruginosa Type VI secretion system toxin Tse8 evolved from a novel N-carbamoylputrescine amidohydrolase.

The polyamine putrescine is synthesized primarily from L-arginine via agmatine in bacteria. There are currently three known routes from agmatine to putrescine, including direct conversion by agmatinase. The other two routes use agmatine deiminase to produce N-carbamoylputrescine from agmatine, then one of two nonhomologous enzymes, putrescine transcarbamylase or N-carbamoylputrescine amidohydrolase (NCPAH), converts N-carbamoylputrescine to putrescine. Here, we functionally identify enzymes from phylogenetically distant bacteria, the ɣ-proteobacterium Shewanella oneidensis, and the actinomycetota species Microterricola gilva, that are novel alternative, nonhomologous, noncanonical NCPAHs that we term AguY, which have emerged by convergent evolution. Kinetic analysis indicates that the AguY enzymes are as efficient as the canonical NCPAH from Pseudomonas aeruginosa in converting N-carbamoylputrescine to putrescine. Genomic evidence suggests that the AguY enzymes may participate in putrescine biosynthetic or agmatine catabolic pathways and are occasionally encoded in genomes that also encode agmatinase. We show that the Type VI secretion system toxin Tse8 from P. aeruginosa has evolved from AguY. It is formally possible that AguY evolved directly or indirectly from the ancient glutamine amidohydrolase GatA, a component of the transamidosome, an RNA/protein complex required for the production of glutamine-charged tRNA. Our study provides a further example of the prevalence of convergent evolution and horizontal gene transfer in polyamine biosynthesis, suggesting pervasive selective pressure to evolve polyamine metabolism in bacteria.

Pseudomonas aeruginosa↗
PubMed2002

Lack of convergence in aquatic Anolis lizards.

Why convergent evolution occurs among some species occupying similar habitats but not among others is a question that has received surprisingly little attention. Caribbean Anolis lizards, known for their extensive convergent evolution among islands in the Greater Antilles, are an appropriate group with which to address this question. Despite the well-documented pattern of between-island convergence, some Greater Antillean anoles are not obviously part of the convergence syndrome. One example involves aquatic anoles--species that are found near to and readily enter streams-which have evolved independently twice in the Caribbean and also twice on mainland Central America. Despite being found in similar habitats, no previous study has investigated whether aquatic anoles represent yet another case of morphological convergence. We tested this hypothesis by collecting morphological data for seven aquatic anole species and 29 species from the six convergent types of Greater Antillean habitat specialists. We failed to find evidence for morphological convergence: the two Caribbean aquatic species are greatly dissimilar to each other and to the Central American species, which, however, may be convergent upon each other. We suggest two possible reasons for this lack of convergence in an otherwise highly convergent system: either there is more than one habitat type occupied by anoles in the proximity of water, or there is more than one way to adapt to a single aquatic habitat. We estimate that almost all of the 113 species of Greater Antillean anoles occupy habitats that are also used by distantly related species, but only 15% of these species are not morphologically similar to their distantly related ecological counterparts. Comparative data from other taxa would help enlighten the question of why the extent of convergence is so great in some lineages and not in others.

Animals↗
PubMed1995

The evolution of sugar isomerases.

L-Arabinose isomerase (EC 5.3.1.4) catalyzes the isomerization of L-arabinose to L-ribulose. Here we report on the purification, kinetic mechanism and chemical mechanism of L-arabinose isomerase from Escherichia coli. The enzyme catalyzes the isomerization of L-arabinose to L-ribulose by a proton transfer mechanism, in contrast to xylose isomerase which uses a hydride transfer mechanism to perform a similar isomerization. Arabinose isomerase activity is metal dependent, although the enzyme can catalyze the exchange of the proton attached to carbon 2 of arabinose with the solvent in the absence of metal ion. Manganese(II) is the only metal ion which renders the enzyme active for the isomerization reaction. Arabinose isomerase has high substrate specificity for L-arabinose. The difference in chemical mechanism between xylose isomerase and arabinose isomerase suggests that these enzymes are not related by convergent evolution. This work also suggests that unless convergent evolution has been demonstrated, the mechanism of one enzyme may not give any insight into the mechanism of a second enzyme catalyzing the same reaction.

Aldose-Ketose Isomerases↗
PubMed1997

Sequence convergence in the peptide-binding region of primate and rodent MHC class Ib molecules.

In addition to the universally expressed and highly polymorphic class Ia genes, the major histocompatibility complex (MHC) of placental mammals includes class Ib genes that are characterized by restricted expression and low levels of sequence polymorphism. The functional importance of class Ib genes as well as their actual function has long been controversial. Phylogenetic analyses have suggested that there are no orthologous relationships among class Ib loci of mammals belonging to different orders, suggesting that these loci have evolved independently since the placental mammals diverged. Here, we present evidence of convergent evolution at the molecular sequence level in the putative peptide-binding regions (PBRs) of human and mouse class Ib genes. So far, there are few if any convincing examples of convergent evolution at the amino acid sequence level, and such evolution is believed to be likely to occur only as a result of strong positive selection. Because the present case involves the functionally important PBR and because the primate and rodent molecules are known to bind similar peptides, this study represents both a convincing case of molecular-level convergence and evidence that MHC class Ib molecules, although not orthologous, may evolve similar functions convergently.

Amino Acid Sequence↗
PubMed2026

Mitogenomic phylogeny of the aquatic subterranean Bathynellacea (Crustacea, Malacostraca) and implications for the monophyly of Syncarida.

The crustacean order Bathynellacea is a specialized monophyletic lineage restricted to aquatic subterranean environments and comprises approximately 340 extant species from three families. Despite advances in sequencing technologies that have significantly increased the number of sequenced crustacean mitogenomes, no bathynellacean mitogenomes have been reported to date. In this study, we report the first complete mitogenomes for Bathynellacea-Allobathynella sp., Arisubathynella cheongmiensis, Hangangbathynella mihoensis (Parabathynellidae), and Bathynella cf. rufa (Bathynellidae)-from two families. These mitogenomes, ranging from 14,422 to 16,645 bp in length, are characterized by extensive gene rearrangements, pronounced compositional biases, and accelerated evolutionary rates. Phylogenetic analyses based on malacostracan mitogenomic data strongly support the monophyly of Bathynellacea. However, the exceptionally long branches separating bathynellacean taxa suggest that extensive morphological simplification, driven by parallel adaptations to subterranean environments, may mask the ancestral diagnostic signals required to resolve their deep-level relationships. Most notably, our results indicate that the two extant orders within the superorder Syncarida-Bathynellacea and Anaspidacea-are phylogenetically distant, supporting the polyphyly of Syncarida. This suggests that their shared morphological features (e.g., the absence of a carapace and the loss of the mandibular lacinia mobilis) are likely products of convergent evolution rather than common ancestry. Our study provides mitogenomic resources for Bathynellacea and underscores the necessity of mitogenomic evidence in reassessing the taxonomic status of subterranean crustacean lineages.

Animals↗
PubMed2004

Evolution of plant parasitism among nematodes.

Despite extraordinary diversity of free-living species, a comparatively small fraction of nematodes are parasites of plants. These parasites represent at least three disparate clades in the nematode tree of life, as inferred from rRNA sequences. Plant parasites share functional similarities regarding feeding, but many similarities in feeding structures result from convergent evolution and have fundamentally different developmental origins. Although Tylenchida rRNA phylogenies are not fully resolved, they strongly support convergent evolution of sedentary endoparasitism and plant nurse cells in cyst and root-knot nematodes. This result has critical implications for using model systems and genomics to identify and characterize parasitism genes for representatives of this clade. Phylogenetic studies reveal that plant parasites have rich and complex evolutionary histories that involve multiple transitions to plant parasitism and the possible use of genes obtained by horizontal transfer from prokaryotes. Developing a fuller understanding of plant parasitism will require integrating more comprehensive and resolved phylogenies with appropriate choices of model organisms and comparative evolutionary methods.

Animals↗
PubMed1982

Living with water stress: evolution of osmolyte systems.

Striking convergent evolution is found in the properties of the organic osmotic solute (osmolyte) systems observed in bacteria, plants, and animals. Polyhydric alcohols, free amino acids and their derivatives, and combinations of urea and methylamines are the three types of osmolyte systems found in all water-stressed organisms except the halobacteria. The selective advantages of the organic osmolyte systems are, first, a compatibility with macromolecular structure and function at high or variable (or both) osmolyte concentrations, and, second, greatly reduced needs for modifying proteins to function in concentrated intracellular solutions. Osmolyte compatibility is proposed to result from the absence of osmolyte interactions with substrates and cofactors, and the nonperturbing or favorable effects of osmolytes on macromolecular-solvent interactions.

Amino Acids↗
PubMed2002

Microbial arsenic: from geocycles to genes and enzymes.

Arsenic compounds have been abundant at near toxic levels in the environment since the origin of life. In response, microbes have evolved mechanisms for arsenic resistance and enzymes that oxidize As(III) to As(V) or reduce As(V) to As(III). Formation and degradation of organoarsenicals, for example methylarsenic compounds, occur. There is a global arsenic geocycle, where microbial metabolism and mobilization (or immobilization) are important processes. Recent progress in studies of the ars operon (conferring resistance to As(III) and As(V)) in many bacterial types (and related systems in Archaea and yeast) and new understanding of arsenite oxidation and arsenate reduction by respiratory-chain-linked enzyme complexes has been substantial. The DNA sequencing and protein crystal structures have established the convergent evolution of three classes of arsenate reductases (that is classes of arsenate reductases are not of common evolutionary origin). Proposed reaction mechanisms in each case involve three cysteine thiols and S-As bond intermediates, so convergent evolution to similar mechanisms has taken place.

Arsenate Reductases↗
PubMed1985

On the probability of the emergence of a protein with a particular function.

Proteins with nearly the same structure and function (homologous proteins) are found in increasing numbers in phylogenetically different, even very distant taxa (e.g. hemoglobins in vertebrates, in some invertebrates, and even in certain plants). In discussing the origin of those proteins biologists hardly at all consider convergent evolution because the origin of proteins is held to be a random process, at least ultimately, since selection can work only what the random process delivers as having a minimum adaptive value. The repetition of a random process with the same result is considered to be extremely unlikely. The supposed (un)likelihood, however, is almost never determined quantitatively. This paper attempts such a quantitative determination. It appears that the probability for the random origin of a definite protein is greater than what one would expect in view of the enormous number of equally possible nucleotide sequences in the corresponding gene since what is equally possible is not always equally likely. The probability, however, of the convergent evolution of two proteins with approximately the same structure and function is too low to be plausible, even when all possible circumstances are present which seem to heighten the likelihood of such a convergence. If this is so, then the plausibility of a random evolution of two or more different but functionally related proteins seems hardly greater.

Amino Acid Sequence↗
PubMed2000

Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences.

Two spurious nodes were found in phylogenetic analyses of vertebrate rhodopsin sequences in comparison with well-established vertebrate relationships. These spurious reconstructions were well supported in bootstrap analyses and occurred independently of the method of phylogenetic analysis used (parsimony, distance, or likelihood). Use of this data set of vertebrate rhodopsin sequences allowed us to exploit established vertebrate relationships, as well as the considerable amount known about the molecular evolution of this gene, in order to identify important factors contributing to the spurious reconstructions. Simulation studies using parametric bootstrapping indicate that it is unlikely that the spurious nodes in the parsimony analyses are due to long branches or other topological effects. Rather, they appear to be due to base compositional bias at third positions, codon bias, and convergent evolution at nucleotide positions encoding the hydrophobic residues isoleucine, leucine, and valine. LogDet distance methods, as well as maximum-likelihood methods which allow for nonstationary changes in base composition, reduce but do not entirely eliminate support for the spurious resolutions. Inclusion of five additional rhodopsin sequences in the phylogenetic analyses largely corrected one of the spurious reconstructions while leaving the other unaffected. The additional sequences not only were more proximal to the corrected node, but were also found to have intermediate levels of base composition and codon bias as compared with neighboring sequences on the tree. This study shows that the spurious reconstructions can be corrected either by excluding third positions, as well as those encoding the amino acids Ile, Val, and Leu (which may not be ideal, as these sites can contain useful phylogenetic signal for other parts of the tree), or by the addition of sequences that reduce problems associated with convergent evolution.

Animals↗
PubMed2004

The crystal structure of feruloyl esterase A from Aspergillus niger suggests evolutive functional convergence in feruloyl esterase family.

As a component of the array of enzymes produced by micro-organisms to deconstruct plant cell walls, feruloyl esterases hydrolyze phenolic groups involved in the cross-linking of arabinoxylan to other polymeric structures. This is important for opening the cell wall structure, making material more accessible to glycosyl hydrolases. Here, we describe the first crystal structure of the non-modular type-A feruloyl esterase from Aspergillus niger (AnFaeA) solved at 2.5A resolution. AnFaeA displays an alpha/beta hydrolase fold similar to that found in fungal lipases and different from that reported for other feruloyl esterases. Crystallographic and site-directed mutagenesis studies allow us to identify the catalytic triad (Ser133-His247-Asp194) that forms the catalytic machinery of this enzyme. The active-site cavity is confined by a lid (residues 68-80), on the analogy of lipases, and by a loop (residues 226-244) that confers plasticity to the substrate-binding site. The lid presents a high ratio of polar residues, which in addition to a unique N-glycosylation site stabilises the lid in an open conformation, conferring the esterase character to this enzyme. A putative model for bound 5,5'-diferulic acid-linked arabinoxylan has been built, pointing to the more relevant residues involved in substrate recognition. Comparison with structurally related lipases reveals that subtle amino acid and conformational changes within a highly conserved protein fold may produce protein variants endowed with new enzymatic properties, while comparison with functionally related proteins points to a functional convergence after evolutionary divergence within the feruloyl esterases family.

Aspergillus niger↗