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PubMed1999

Contribution of gene conversion in the evolution of the human beta-like globin gene family.

Gene conversion is referred to as one of two types of mechanisms known to act on gene families, mainly to maintain their sequence homogeneity or, in certain cases, to produce sequence diversity. The concept of gene conversion was established 20 years ago by researchers working with fungi. A few years later, gene conversion was also observed in the human genome, i.e. the gamma-globin locus. The aim of this article is to emphasize the role of genetic recombination, particularly of gene conversion, in the evolution of the human beta-like globin genes and further to summarize its contribution to the convergent evolution of the fetal globin genes. Finally, this article attempts to re-examine the origin and spread of specific mutations of the beta-globin cluster, such as the sickle cell or beta-thalassemia mutations, on the basis of repeated gene conversion events.

Animals↗
PubMed2006

Histology and immunology of the placenta in the Atlantic sharpnose shark, Rhizoprionodon terraenovae.

The Atlantic sharpnose shark, Rhizoprionodon terraenovae, is viviparous species that forms a yolk sac placenta to facilitate exchange between mother and embryo. However, very little is known about the immunological aspects of this organ in sharks. To begin to understand this, we used histology, histochemistry and immunohistochemistry to investigate the sharpnose shark placenta throughout gestation. We report the presence of lymphoid aggregates in the maternal portion of the placenta during all stages of gestation, and their increasing size and vascularity near term. Immunoglobulin is found in the maternal tissues of the placenta, but its presence in embryonic tissue and potential transfer from maternal circulation remains unclear. Placental cells resembling mammalian uterine NK cells and melanomacrophages of lower vertebrates are described for the first time. Similarities with mammalian placentae point to shared aspects in the co-evolution of reproductive and immune systems, even between two phylogenetically diverse groups in which placentation arose by convergent evolution.

Animals↗
PubMed1979

Contrasted modes of evolution in the same genome: allozymes and adaptive change in Heliconius.

Butterflies in the South American genus Heliconius have undergone a spectacular adaptive radiation (with convergent evolution between some lines) in their color patterns; this has been produced by natural selection for muellerian mimicry. The genetic basis of this radiation, shown by crossing highly differentiated races within two of the species, is homozygosity for alternative alleles at some half dozen loci. In complete contrast, allozyme loci in these butterflies are strongly heterozygous and show only frequency differences (never amounting to homozygosity of alternative alleles) between races; the amount of allozyme divergence is the same between races of H. erato and H. sara, although in color pattern the first forms marked races and the other does not. For the allozymes, there is a strong correlation over loci for rate of divergence between species and average heterozygosity. This is not true of the genes controlling color pattern. Heterozygosity of the enzymes is correlated with subunit molecular weight. Thus, different parts of the genome can evolve in different ways simultaneously; genes controlling color pattern in the "classical" mode, and allozymes in a different mode in which the rate of evolution is related to their heterozygosity (a "balance" or "neutral" mode).

Animals↗
PubMed2005

Mapping stem cell activities in the feather follicle.

It is important to know how different organs 'manage' their stem cells. Both hair and feather follicles show robust regenerative powers that episodically renew the epithelial organ. However, the evolution of feathers (from reptiles to birds) and hairs (from reptiles to mammals) are independent events and their follicular structures result from convergent evolution. Because feathers do not have the anatomical equivalent of a hair follicle bulge, we are interested in determining where their stem cells are localized. By applying long-term label retention, transplantation and DiI tracing to map stem cell activities, here we show that feather follicles contain slow-cycling long-term label-retaining cells (LRCs), transient amplifying cells and differentiating keratinocytes. Each population, located in anatomically distinct regions, undergoes dynamic homeostasis during the feather cycle. In the growing follicle, LRCs are enriched in a 'collar bulge' niche. In the moulting follicle, LRCs shift to populate a papillar ectoderm niche near the dermal papilla. On transplantation, LRCs show multipotentiality. In a three-dimensional view, LRCs are configured as a ring that is horizontally placed in radially symmetric feathers but tilted in bilaterally symmetric feathers. The changing topology of stem cell activities may contribute to the construction of complex feather forms.

Animals↗
PubMed2005

Divergent evolution within protein superfolds inferred from profile-based phylogenetics.

Many dissimilar protein sequences fold into similar structures. A central and persistent challenge facing protein structural analysis is the discrimination between homology and convergence for structurally similar domains that lack significant sequence similarity. Classic examples are the OB-fold and SH3 domains, both small, modular beta-barrel protein superfolds. The similarities among these domains have variously been attributed to common descent or to convergent evolution. Using a sequence profile-based phylogenetic technique, we analyzed all structurally characterized OB-fold, SH3, and PDZ domains with less than 40% mutual sequence identity. An all-against-all, profile-versus-profile analysis of these domains revealed many previously undetectable significant interrelationships. The matrices of scores were used to infer phylogenies based on our derivation of the relationships between sequence similarity E-values and evolutionary distances. The resulting clades of domains correlate remarkably well with biological function, as opposed to structural similarity, indicating that the functionally distinct sub-families within these superfolds are homologous. This method extends phylogenetics into the challenging "twilight zone" of sequence similarity, providing the first objective resolution of deep evolutionary relationships among distant protein families.

Evolution, Molecular↗
PubMed2003

Evolution of function in (beta/alpha)8-barrel enzymes.

The (beta/alpha)(8)-barrel is the most common fold in structurally characterized enzymes. Whether the functionally diverse enzymes that share this fold are the products of either divergent or convergent evolution (or both) is an unresolved question that will probably be answered as the sequence databases continue to expand. Recent work has examined natural, designed, and directed evolution of function in several superfamilies of (beta/alpha)(8)-barrel containing enzymes.

Animals↗
PubMed2006

Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale.

Consideration of the scale at which communities are defined both taxonomically and spatially can reconcile apparently contradictory results on the extent to which plants show phylogenetic niche conservatism. In plant communities in north central Florida, we collected species abundances in 55 0.1-ha plots in several state parks. When communities were defined narrowly to include a single phylogenetic lineage, such as Quercus, Pinus, or Ilex, neighbors tended to be less related than expected (phylogenetic overdispersion) or there was no pattern. If the same communities were defined more broadly, such as when all seed plants were included, neighbors tended to be more related than expected (phylogenetic clustering). These results provide evidence that species interactions among close relatives influence community structure, but they also show that niche conservatism is increasingly evident as communities are defined to include greater phylogenetic diversity. We also found that, as the spatial scale is increased to encompass greater environmental heterogeneity, niche conservatism emerges as the dominant pattern. We then examined patterns of trait evolution in relation to trait similarity within communities for 11 functional traits for a single phylogenetic lineage (Quercus) and for all woody plants. Among the oaks, convergent evolution of traits important for environmental filtering contributes to the observed pattern of phylogenetic overdispersion. At the broader taxonomic scale, traits tend to be conserved, giving rise to phylogenetic clustering. The shift from overdispersion to clustering can be explained by the increasing conservatism of traits at broader phylogenetic scales.

Biological Evolution↗
PubMed2005

Comparative analysis and insights into the evolution of gene clusters for glycopeptide antibiotic biosynthesis.

The bal, cep, dbv, sta and tcp gene clusters specify the biosynthesis of the glycopeptide antibiotics balhimycin, chloroeremomycin, A40926, A47934 and teicoplanin, respectively. These structurally related compounds share a similar mechanism of action in their inhibition of bacterial cell wall formation. Comparative sequence analysis was performed on the five gene clusters. Extensive conserved synteny was observed between the bal and cep clusters, which direct the synthesis of very similar compounds but originate from two different species of the genus Amycolatopsis. All other cluster pairs show a limited degree of conserved synteny, involving biosynthetically functional gene cassettes: these include those involved in the synthesis of the carbon backbone of two non-proteinogenic amino acids; in the linkage of amino acids 1--3 and 4--7 in the heptapeptide; and in the formation of the aromatic cross-links. Furthermore, these segments of conserved synteny are often preceded by conserved intergenic regions. Phylogenetic analysis of protein families shows several instances in which relatedness in the chemical structure of the glycopeptides is not reflected in the extent of the relationship of the corresponding polypeptides. Coherent branchings are observed for all polypeptides encoded by the syntenous gene cassettes. These results suggest that the acquisition of distinct, functional genetic elements has played a significant role in the evolution of glycopeptide gene clusters, giving them a mosaic structure. In addition, the synthesis of the structurally similar compounds A40926 and teicoplanin appears as the result of convergent evolution.

Actinomycetales↗
PubMed1996

Peptide binding function and the paradox of HLA disease associations.

Many studies have found associations between HLA loci and susceptibility or resistance to both infectious and autoimmune diseases, but often subsequent studies fail to find the same association. Such inconsistencies are not surprising if we consider what is known of the population biology and evolution of HLA genes, especially the consequences of natural selection favouring heterozygosity in the peptide binding regions (PBR) of HLA molecules. Because of past recombination event and/or convergent evolution, alleles that are not closely related in overall sequence may come to resemble each other in the PBR. Because peptide binding is likely to be important for the role of HLA molecules in both infectious and autoimmune disease, a strategy of searching for HLA disease associations that groups alleles in functional categories based on PBR motifs may prove more successful than conventional strategies. Likewise, in developing approaches for molecular typing, it may be advisable to develop methods that group alleles on the basis of shared PBR motifs rather than simply on the basis of shared primer sites in less functionally important regions.

Animals↗
PubMed2000

Evolution of gall morphology and host-plant relationships in willow-feeding sawflies (Hymenoptera: Tenthredinidae).

There are over 200 species of nematine sawflies that induce galls on willows (Salix spp.). Most of the species are mono- or oligophagous, and they can be separated into seven or eight different groups based on the type of gall that they induce. We studied the evolution of different gall types and host plant associations by reconstructing the phylogeny of five outgroup and 31 ingroup species using DNA sequence data from the mitochondrial cytochrome b gene. Maximum-parsimony and maximum-likelihood analyses resulted in essentially the same phylogeny with high support for important branches. The results show that: (1) the galling species probably form a monophyletic group; (2) true closed galls evolved only once, via leaf folders; (3) with the possible exception of leaf rollers, all gall type groups are mono- or paraphyletic; (4) similar gall types are closer on the phylogeny than would be expected by a random process; (5) there is an apparent evolutionary trend in galling site from the leaf edge towards the more central parts of the host plant; and (6) many willow species have been colonized several times, which excludes the possibility of parallel cladogenesis between willows and the gallers; however, there are signs of restrictions in the evolution of host use. Many of the patterns in the evolutionary history of nematine gallers have also been observed in earlier studies on other insect gallers, indicating convergent evolution between the independent radiations.

Animals↗
PubMed1997

[Structures and functions of animal toxins].

This brief review is devoted to the presentation of the major toxic proteins found in venoms of animals from five phyla. It is shown that various groups of venomous animals, including scorpions and snakes, produce toxins that exert different functions although they adopt a similar structure, suggesting that these toxins result from a divergent evolution. On the opposite, it is shown that toxins produced by animals from different phyla can exert similar functions even though they adopt unrelated structures, suggesting a convergent evolution. Finally, this review describes, at the molecular level, the functional and structural properties, including the dynamical characteristics, of a snake toxin which binds to the peripheral nicotinic acetylcholine receptor.

Animals↗
PubMed1999

Molecular phylogenetics and the evolution of labral spines among eastern Pacific ocenebrine gastropods.

Labral spines are sharp projections of the apertural lip found in some marine gastropods that are used to penetrate hard-shelled prey. The majority of gastropod genera that contain labral spine-bearing species are found in the subfamily Ocenebrinae (Gastropoda: Muricidae). To reconstruct the evolutionary history of labral spine-bearing and labral spine-lacking gastropods in the eastern Pacific (EP) Ocean, partial sequences of two mitochondrial genes (cytochrome oxidase I and 12S rRNA) were obtained from representative taxa. Despite high nucleotide bias, a variety of phylogenetic reconstruction methods produced the same tree topology. The traditional taxonomic view that all "Nucella-like" spine-bearing taxa in the EP belong to a monophyletic "Acanthina" is rejected due to nonmonophyly of this group. The more recently recognized "Acanthinucella" is also not monophyletic, and we therefore propose the new genus Mexacanthina for two Mexican species formerly assigned to Acanthinucella. The genus Ocinebrina, which first appears in the middle Eocene, is not a stem EP ocenebrine lineage and may also not be a monophyletic clade. Tracing the evolutionary history of labral spines among extant lineages indicates that the absence of a labral spine is ancestral for all EP ocenebrines. Ancestral conditions could not be resolved unambiguously for all nodes of the phylogeny based on extant taxa. However, by jointly considering both molecular phylogenetic relationships and the phylogenetic affinities of several extinct taxa, all remaining character state transformation can be inferred unambiguously. Based on this analysis, a labral spine likely evolved independently in at least four lineages of EP ocenebrines. Although homoplasy appears to characterize labral spine evolution among ocenebrine gastropods, the structural position of a labral spine was evolutionarily altered in one lineage, indicating that different types of labral spines do not necessarily reflect convergent evolution.

Animals↗
PubMed2004

Evolution of coral pigments recreated.

In proteins homologous to the green fluorescent protein (GFP), formation of red fluorescence requires three autocatalytic steps, whereas only two are needed for green fluorescence. Multiple red/green color diversification events in the GFP superfamily may reflect convergent evolution of the more complex three-step pathway. In the great star coral Montastraea cavernosa, a recreated common ancestor of green and red proteins turned out to be green, indicating that in this case red proteins evolved their color independently from most other homologous red proteins. Furthermore, red color appears to have evolved gradually by small incremental transitions.

Amino Acid Sequence↗
PubMed1995

Gene products of Escherichia coli: sequence comparisons and common ancestries.

Sequences of 1,862 chromosomally encoded Escherichia coli K12 proteins were examined to identify genes likely to have arisen by duplication of genes in an ancestral chromosome. The criteria for sequence relatedness were an alignment of at least 100 amino acid residues and a PAM distance (number of accepted point mutations per 100 residues separating two sequences) below 250. A total of 971 of the 1,862 proteins examined were found in 2,329 sequence-related pairs that met these criteria. Most proteins of the sequence-related pairs were related in cellular function, as judged by biochemical and/or physiological features. Many of the pairs of proteins could be grouped into sequence-related families. If such groupings were generated from ancestral genes by duplication and divergence events, through these sequence comparisons we can identify putative ancestral sequences of the present-day genes of E. coli and other organisms. The results suggest that the 971 paralogous genes could have been derived from only 204 ancestral genes. We have also shown that the process of duplication and divergence is not the exclusive mechanism of evolution of all E. coli genes. Indeed, the relationships among the sequences of multiple (in the sense of redundant) enzymes indicate that nearly half could have arisen either by convergent evolution or by lateral transfer. Therefore, not all functionally related genes need arise by duplication and divergence.

Bacterial Proteins↗
PubMed2006

The phylogenetic pattern of speciation and wing pattern change in neotropical Ithomia butterflies (Lepidoptera: nymphalidae).

Species level phylogenetic hypotheses can be used to explore patterns of divergence and speciation. In the tropics, speciation is commonly attributed to either vicariance, perhaps within climate-induced forest refugia, or ecological speciation caused by niche adaptation. Mimetic butterflies have been used to identify forest refugia as well as in studies of ecological speciation, so they are ideal for discriminating between these two models. The genus Ithomia contains 24 species of warningly colored mimetic butterflies found in South and Central America, and here we use a phylogenetic hypothesis based on seven genes for 23 species to investigate speciation in this group. The history of wing color pattern evolution in the genus was reconstructed using both parsimony and likelihood. The ancestral pattern for the group was almost certainly a transparent butterfly, and there is strong evidence for convergent evolution due to mimicry. A punctuationist model of pattern evolution was a significantly better fit to the data than a gradualist model, demonstrating that pattern changes above the species level were associated with cladogenesis and supporting a model of ecological speciation driven by mimicry adaptation. However, there was only one case of sister species unambiguously differing in pattern, suggesting that some recent speciation events have occurred without pattern shifts. The pattern of geographic overlap between clades over time shows that closely related species are mostly sympatric or, in one case, parapatric. This is consistent with modes of speciation with ongoing gene flow, although rapid range changes following allopatric speciation could give a similar pattern. Patterns of lineage accumulation through time differed significantly from that expected at random, and show that most of the extant species were present by the beginning of the Pleistocene at the latest. Hence Pleistocene refugia are unlikely to have played a major role in Ithomia diversification.

Animals↗
PubMed1994

Darwinian evolution patterns in food products and beverages.

Although the development and survival of food products are regulated by mechanisms that bear little resemblance to those operating in the living world, their general evolutionary patterns share certain common features. These include punctuated equilibria, convergent evolution, the coevolution, the equivalence of symbiosis, and, rarely, even parasitism. The evolution of food products, like that of living organisms and other systems, is a nonlinear process. Consequently, its path can be affected not only by major events that drastically alter the environment but also by very minor events that may be unnoticeable at the time of their occurrence.

Animals↗
PubMed2002

Evolution of the visual cycle: the role of retinoid-binding proteins.

The trafficking of retinoids in the retina represents a model to study soluble hormone-binding proteins in a complex system subject to profound evolutionary adaptations. Although a remarkable illustration of convergent evolution, all visual systems detect light in the same way, that is through the photoisomerization of an 11-cis retinoid to a corresponding trans isomer. What is strikingly different between the systems, is the mechanism by which the 11-cis chromophore is reformed and visual pigment regenerated in a process known as the visual cycle. The variations of the cycle address a problem inherent to retinoids themselves. That is, the properties that make these molecules suited for light detection also account for their susceptibility to oxidative and isomeric degradation, and cellular toxicity. The cycle therefore provides an opportunity to examine the role of soluble hormone-binding proteins within an integrative and evolutionary context. The present review focuses on interphotoreceptor retinoid-binding protein (IRBP), a controversial glycolipoprotein that recruits a protein fold common to Cterminal-processing proteases and the crotonase family. This unorthodox retinoid-binding protein is entrapped in the subretinal compartment of those eyes that translocate visual cycle retinoids between the photoreceptors and the retinal pigment epithelium. Recent studies suggest that we should look beyond a strictly carrier function if we are to appreciate the role of IRBP in the visual cycle. Here we draw lessons from other soluble hormone-binding proteins to anticipate avenues of future research likely to provide insight into the structure and function of IRBP in vision.

Amino Acid Sequence↗
PubMed1992

Chromosomal rearrangements in rock wallabies, Petrogale (Marsupialia: Macropodidae). VII. G-banding analysis of Petrogale brachyotis and P. concinna: species with dramatically altered karyotypes.

G-banded metaphase preparations of cultured fibroblasts were used to construct the karyotypes of Petrogale brachyotis (2n = 18) and P. concinna (2n = 16). The two karyotypes differ significantly from the plesiomorphic karyotype of the genus and from those of all other Petrogale species examined. Petrogale brachyotis and P. concinna are characterised by three synapomorphies: a 1-10 centric fusion, a 3a-6 centric fusion, and a submetacentric chromosome 2 (2s). Both species also possess autapomorphies. Petrogale brachyotis is characterised by submetacentric chromosomes 5 (5s) and 4 (4sm), whereas P. concinna is characterised by a 5-9 centric fusion and a submetacentric chromosome 8 (8m). The 2s, 5s, 4sm, and 8m chromosomes all appear to be derived from their plesiomorphic homologs by centromeric transpositions. Although the rate of chromosome evolution varies considerably in Petrogale, the genus clearly exhibits karyotypic orthoselection, with all the autosomal rearrangements identified being either centric fusions or centromeric transpositions. This study also illustrates the potential for convergent evolution in chromosomally diverse groups and demonstrates the importance of G-banding studies for accurate identification of chromosome rearrangements.

Animals↗