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.      

Convergent and parallel evolution: a model illustrating selection, phylogeny and phenetic similarity

A model is proposed which considers the structural relationships of body characteristics and their role in a concept wherein the phylogenetic relationship of the organisms under study is interpreted as constituting degrees of convergent or parallel evolution. The model also accounts for the relationships between selection pressures, phylogeny, and phenetic expression. The phenomena of convergent and parallel evolution are based upon the observations of similar characteristics, the geometric concept, magnitude and similarity of selection pressures, and the phylogenetic relationship of the groups in question.     

Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution

HLA class I molecules can be classified into supertypes associated with overlapping peptide-binding motifs and repertoires. Herein, overlaps in peptide-binding and T-cell recognition repertoires were demonstrated between mouse and human molecules. Since rodent and primate lineages separated before the current allelic variation of mouse and human class I molecules, these data demonstrate that supertypic specificities originated by convergent evolution. Phylogenetic and structural analyses demonstrated that convergent evolution also occurs amongst primates and within the human species, resulting from the selection of different pocket structures having similar specificity or independent repeated selection of the same pocket structure.     

Hinged teeth for hard-bodied prey: a case of convergent evolution between snakes and legless lizards

Savitzky (1981) described hinged teeth in several taxa of snakes, and interpreted this type of dentition as an adaptation to feeding on hard-bodied prey (scincid lizards). We tested this hypothesis by examining the dentition of insectivorous and saurophagous members of the Australian legless lizards, Pygopodidae. Insectivorous taxa ( Delma, Pygopus ) have peg-like pleurodont dentition, but the saurophagous Lialis has slender, recurved, sharply-pointed teeth, like those of many snakes. The teeth of Lialis are 'hinged' on their supporting bones: each tooth folds when pressure is applied to its anterior surface, but locks in an erect position when forced from behind, The tooth hinge is probably collagenous, and does not contain elastin. The presence of hinged teeth in Lids , which feeds predominately on scincid lizards, offers strong support for Savitzky's hypothesis.     

Structural plasmid evolution as a result of coupled recombinations at bom and cer sites

We have studied the recombination of plasmids bearing bom and cer sites. The bom ( basis of mobilization) site is required for conjugative transfer, while the cer ( Col E1 resolution) site is involved in the resolution of plasmid multimers, which increases plasmid stability. We constructed a pair of parent plasmids in such a way as to allow us select clones containing recombinant plasmids directly. Clone selection was based on the McrA sensitivity of recipient host DNA modified by M. Ecl18kI, which is encoded by one of the parent plasmids. The recombinant plasmid contains segments originating from both parental DNAs, which are bounded by bom and cer sites. Its structure is in accordance with our previously proposed model for recombination mediated by bom and cer sequences. The frequency of recombinant plasmid formation coincided with the frequency of recombination at the bom site. We also show that bom-mediated recombination in trans, unlike in cis, is independent of other genetic determinants on the conjugative plasmids.     

Laticiferous taxa as a source of energy and hydrocarbon

Twenty-nine laticiferous taxa of Apocynaceae, Asclepiadaceae, and Sapotaceae were screened for suitability as alternative sources of renewable energy, rubber, and phytochemicals and to select the most promising ones for large-scale cultivation. Of these,Allamanda violacea (14.9% protein, 13.8% polyphenol, 8.6% oil, 3.2% hydrocarbon),Catharanthus roseus (15.4% protein, 10.4% polyphenol, 11.5% oil, 1.9% hydrocarbon), andHolarrhena antidysenterica (14.2% protein, 16.4% polyphenol, 5.4% oil, 4.8% hydrocarbon) of Apocynaceae;Asclepias curassavica (19.3% protein, 6.5% polyphenol, 3.9% oil, 2.0% hydrocarbon), Calotropis gigantea (18.5% protein, 6.8% polyphenol, 7.0% oil, 2.8% hydrocarbon) of Asclepiadaceae;Mimusops elengi (11.3% protein, 9.7% polyphenol, 7.2% oil, 4.0% hydrocarbon) of Sapotaceae show promising potential for future petrochemical plantations; of all these taxa,Holarrhena antidysenterica yielded an unusually high percentage (4.8%) of hydrocarbon fraction followed byMimusops elengi (4.0%). NMR spectra confirmed the presence of cis-polyisoprene in all species studied exceptNerium indicum (white-flowered var.). These data indicate that the majority of the species under investigation may be considered for large-scale cultivation as an alternative source of rubber, intermediate energy, and other phytochemicals.     

Conservation and evolution of microsatellite loci in primate taxa

Microsatellites are promising genetic markers for the study of demographic structure and phylogenetic history in populations. However, little information exists on the molecular nature of the repeats and their flanking sequences of a same microsatellite in a large range of species. In this study, we report polymorphism and consensus sequences of eight microsatellite loci using human primers in 20 primate species. The results show size polymorphism in almost all species and microsatellites. These loci are therefore useful markers for population genetic studies between populations of the same species. Insertion/deletion events are frequent in the flanking regions, the majority concerning several contiguous bases. This is in contrast with the more usual single base pair events in non-coding regions. The ranges of allele lengths in non-human primates often show no overlap with that of human, usually due to the deletion/insertion events in the flanking sequences, producing smaller allele lengths rather than smaller numbers of repeats. The use of length of PCR product will bias the inter-species interpretation reducing the number of observable alleles and treating as the same allele very divergent molecular sequences. Caution should be used when employing microsatellites in cross-species comparisons in which the species under study are separated by significant amounts of evolutionary time: in such cases allele comparison cannot be based on lengths alone.     

Bat echolocation calls: adaptation and convergent evolution

Bat echolocation calls provide remarkable examples of 'good design' through evolution by natural selection. Theory developed from acoustics and sonar engineering permits a strong predictive basis for understanding echolocation performance. Call features, such as frequency, bandwidth, duration and pulse interval are all related to ecological niche. Recent technological breakthroughs have aided our understanding of adaptive aspects of call design in free-living bats. Stereo videogrammetry, laser scanning of habitat features and acoustic flight path tracking permit reconstruction of the flight paths of echolocating bats relative to obstacles and prey in nature. These methods show that echolocation calls are among the most intense airborne vocalizations produced by animals. Acoustic tracking has clarified how and why bats vary call structure in relation to flight speed. Bats using broadband echolocation calls adjust call design in a range-dependent manner so that nearby obstacles are localized accurately. Recent phylogenetic analyses based on gene sequences show that particular types of echolocation signals have evolved independently in several lineages of bats. Call design is often influenced more by perceptual challenges imposed by the environment than by phylogeny, and provides excellent examples of convergent evolution. Now that whole genome sequences of bats are imminent, understanding the functional genomics of echolocation will become a major challenge.     

Floral scent in bat-pollinated plants: a case of convergent evolution

The chemical composition of floral scent in eight bat-pollinated species belonging to six different plant families was investigated. Floral scent was collected by headspace trapping using porous adsorbents and the chemical composition determined by coupled gas chromatography-mass spectrometry. In all species except one the floral scent was found to include sulphur-containing compounds, of which several are reported for the first time in floral scents. Three species contained mushroom-like smelling fatty acid derivatives with a C₈-skeleton. Such flowers may be recognized by pollinators as humid environments in otherwise dry surroundings. The presence of similar or chemically closely related sulphur containing compounds in floral scent of bat-pollinated plant species from differing families may represent a case of convergent evolution in scent composition and an adaptation to attract this specific group of pollinators with similar sensory preferences.     

Genetic architecture underlying convergent evolution of egg-laying behavior in a seed-feeding beetle

Independent populations subjected to similar environments often exhibit convergent evolution. An unresolved question is the frequency with which such convergence reflects parallel genetic mechanisms. We examined the convergent evolution of egg-laying behavior in the seed-feeding beetle Callosobruchus maculatus. Females avoid ovipositing on seeds bearing conspecific eggs, but the degree of host discrimination varies among geographic populations. In a previous experiment, replicate lines switched from a small host to a large one evolved reduced discrimination after 40 generations. We used line crosses to determine the genetic architecture underlying this rapid response. The most parsimonious genetic models included dominance and/or epistasis for all crosses. The genetic architecture underlying reduced discrimination in two lines was not significantly different from the architecture underlying differences between geographic populations, but the architecture underlying the divergence of a third line differed from all others. We conclude that convergence of this complex trait may in some cases involve parallel genetic mechanisms.     

Glutaminyl cyclases from animals and plants: a case of functionally convergent protein evolution

Several mammalian peptide hormones and proteins from plant and animal origin contain an N-terminal pyroglutamic acid (pGlu) residue. Frequently, the moiety is important in exerting biological function in either mediating interaction with receptors or stabilizing against N-terminal degradation. Glutaminyl cyclases (QCs) were isolated from different plants and animals catalyzing pGlu formation. The recent resolution of the 3D structures of Carica papaya and human QCs clearly supports different evolutionary origins of the proteins, which is also reflected by different enzymatic mechanisms. The broad substrate specificity is revealed by the heterogeneity of physiological substrates of plant and animal QCs, including cytokines, matrix proteins and pathogenesis-related proteins. Moreover, recent evidence also suggests human QC as a catalyst of pGlu formation at the N-terminus of amyloid peptides, which contribute to Alzheimer's disease. Obviously, owing to its biophysical properties, the function of pGlu in plant and animal proteins is very similar in terms of stabilizing or mediating protein and peptide structure. It is possible that the requirement for catalysis of pGlu formation under physiological conditions may have triggered separate evolution of QCs in plants and animals.     

A parallel between development and evolution: Germ cell recruitment by the gonads

In gonad-bearing animals gametogenesis can be divided into three main phases. During embryonic development the primordial gem cells move towards the gonadal primordia. A long, intra-gonadal phase follows during which the germ cells grow and differentiate. Mature germ cells are finally released from the gonads and brought to the exterior. Thus, germ cells are successively motile, non-motile and motile again. This complex life history is given here a simple evolutionary interpretation. The basic assumption is that primitive Metazoa already had germ cells, but no gonads to harbour them. Higher animals acquired gonads, which sequestered the germ cells, thus creating the temporary confinement experienced by germ cells in most present-day Metazoa. This evolutionalry scheme may explain why several steps of germ cell differentation are totally or partially independent of the gonads. These steps presumably existed in primitive, gonad-free Metazoa, and conserved their autonomy in higher animals.     

Relationship between pycnotic indec Qp as a result of oxygen supply and similar indices as a result of in vitro offer of cytochrome c and NADP in psychiatry.

The authors follow up on their previous studies of morphological changes in the properties of white blood cells represented by the oxygen pycnotic index Qp in patients with the schizophrenic syndrome. Several years of research made it obvious to them that this index remains generally unaffected by drugs administered during the treatment although the patient does show a pronounced clinical change. They decided to substitute the offer of oxygen by adding a supply of cytochrome c and NADP, i.e. by substances that give a boost to the oxidoreduction processes within the cell. They found the pycnotic quotient, based on cytochrome c, and - to an even greater degree - the NADP-based quotient to be more responsive to differences in the seriousness of the disease than the oxygen quotient.