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PubMed2005

Gain and loss of multiple genes during the evolution of Helicobacter pylori.

Sequence diversity and gene content distinguish most isolates of Helicobacter pylori. Even greater sequence differences differentiate distinct populations of H. pylori from different continents, but it was not clear whether these populations also differ in gene content. To address this question, we tested 56 globally representative strains of H. pylori and four strains of Helicobacter acinonychis with whole genome microarrays. Of the weighted average of 1,531 genes present in the two sequenced genomes, 25% are absent in at least one strain of H. pylori and 21% were absent or variable in H. acinonychis. We extrapolate that the core genome present in all isolates of H. pylori contains 1,111 genes. Variable genes tend to be small and possess unusual GC content; many of them have probably been imported by horizontal gene transfer. Phylogenetic trees based on the microarray data differ from those based on sequences of seven genes from the core genome. These discrepancies are due to homoplasies resulting from independent gene loss by deletion or recombination in multiple strains, which distort phylogenetic patterns. The patterns of these discrepancies versus population structure allow a reconstruction of the timing of the acquisition of variable genes within this species. Variable genes that are located within the cag pathogenicity island were apparently first acquired en bloc after speciation. In contrast, most other variable genes are of unknown function or encode restriction/modification enzymes, transposases, or outer membrane proteins. These seem to have been acquired prior to speciation of H. pylori and were subsequently lost by convergent evolution within individual strains. Thus, the use of microarrays can reveal patterns of gene gain or loss when examined within a phylogenetic context that is based on sequences of core genes.

Evolution, Molecular↗
PubMed2002

On the evolution of programmed cell death: apoptosis of the unicellular eukaryote Leishmania major involves cysteine proteinase activation and mitochondrion permeabilization.

Leishmania major is a protozoan parasite from one of the most ancient phylogenic branches of unicellular eukaryotes, and containing only one giant mitochondrion. Here we report that staurosporine, that induces apoptosis in all mammalian nucleated cells, also induces in L. major a death process with several cytoplasmic and nuclear features of apoptosis, including cell shrinkage, phosphatidyl serine exposure, maintenance of plasma membrane integrity, mitochondrial transmembrane potential (DeltaPsim) loss and cytochrome c release, nuclear chromatin condensation and fragmentation, and DNA degradation. Nuclear apoptosis-like features were prevented by cysteine proteinase inhibitors, and cell free assays using dying L. major cytoplasmic extracts indicated that the cysteine proteinases involved (i) also induced nuclear apoptosis-like features in isolated mammalian nuclei, and (ii) shared at least two nuclear substrates, but no cleavage site preference, with human effector caspases. Finally, isolated L. major mitochondria released cytochrome c and cysteine proteinases with nuclear pro-apoptotic activity when incubated with human recombinant Bax, even (although much less efficiently) when Bax was deleted of its transmembrane domain required for insertion in mitochondrial outermembranes, implying that L. major mitochondrion may express proteins able to interact with Bax. The recruitment of cysteine proteinases and mitochondria to the cell death machinery may be of very ancient evolutionary origin. Alternately, host/parasite interactions may have exerted selective pressures on the cell death phenotype of kinetoplastid parasites, resulting in the more recent emergence of an apoptotic machinery through a process of convergent evolution.

Animals↗
PubMed1998

Correlations of cranial morphology, ecology, and evolution in Australian suctorial tadpoles of the genera Litoria and Nyctimystes (Amphibia: Anura: Hylidae: Pelodryadinae).

Suctorial anuran larvae are highly specialized for living in fast-flowing waters, using their oral disks as adhesive organs to attach to the substrate. The cranial musculoskeletal structure of suctorial larvae of Litoria nannotis, L. rheocola, and Nyctimystes dayi (Hylidae: Pelodryadinae) were compared with congenerics with pond-type larvae (L. caerulea, L. genimaculata, L. xanthomera). Data from two other neobatrachian species with suctorial larvae (Boophis sp., Hyla armata) as well as published descriptions were taken into account. Suctorial tadpoles evolved several times independently in the Neobatrachia and share various features, irrespective of their phylogenetic position. These include the following. Cornua trabeculae are expanded anteriorly and sometimes fused. The lower jaws are robust. The greatest width of the skull is at the level of the jaw articulation. The upper jaw cartilages are partially or fully fused. The palatoquadrate is robust and connected to the skull by a wide commissura quadratocranialis anterior, processus oticus, processus basalis (in some species), and processus ascendens (vestigial or absent in some species). A processus ventralis quadrati provides an extended area of origin for the m. orbitohyoideus. The m. rectus abdominis inserts far anterior and acts on the cranium. The insertion of the epaxial musculature is shifted anteriorly to the anterior parts of the otic capsule. The mm. diaphragmatobranchialis and rectus cervicis cross at their origins. The origin of the m. levator mandibulae anterior has shifted posteriorly. The branchial basket is relatively small and the ceratohyal area is large. Multiple convergent evolution of these features suggests that they may be causally associated with the suctorial mode of larval life. Aside from these characters, however, the suctorial and pond-type neobatrachian species are remarkably similar in their jaw musculature and hyobranchial musculoskeletal composition. In some features, Ascaphus truei differs significantly from the neobatrachian suctorial species, indicating the influence of the historically distant separation of the two taxa. A novel modification of the upper jaw abduction mechanism has evolved in L. nannotis, L. rheocola, and N. dayi. It involves an adrostral cartilage as a pushing-rod element. This mechanism and unique structural similarities of the cartilago labialis superior gives support to the preliminary assumption that the nannotis species group is more closely related to the suctorial Nyctimystes dayi than it is to other Litoria species with pond-type larvae. Suctorial larvae presumably were present in the most recent common ancestor of the Litoria nannotis group and Nyctimystes dayi.

Animals↗
PubMed2005

Non-neural ectoderm is really neural: evolution of developmental patterning mechanisms in the non-neural ectoderm of chordates and the problem of sensory cell homologies.

In chordates, the ectoderm is divided into the neuroectoderm and the so-called non-neural ectoderm. In spite of its name, however, the non-neural ectoderm contains numerous sensory cells. Therefore, the term "non-neural" ectoderm should be replaced by "general ectoderm." At least in amphioxus and tunicates and possibly in vertebrates as well, both the neuroectoderm and the general ectoderm are patterned anterior/posteriorly by mechanisms involving retinoic acid and Hox genes. In amphioxus and tunicates the ectodermal sensory cells, which have a wide range of ciliary and microvillar configurations, are mostly primary neurons sending axons to the CNS, although a minority lack axons. In contrast, vertebrate mechanosensory cells, called hair cells, are all secondary neurons that lack axons and have a characteristic eccentric cilium adjacent to a group of microvilli of graded lengths. It has been highly controversial whether the ectodermal sensory cells in the oral siphons of adult tunicates are homologous to vertebrate hair cells. In some species of tunicates, these cells appear to be secondary neurons, and microvillar and ciliary configurations of some of these cells approach those of vertebrate hair cells. However, none of the tunicate cells has all the characteristics of a hair cell, and there is a high degree of variation among ectodermal sensory cells within and between different species. Thus, similarities between the ectodermal sensory cells of any one species of tunicate and craniate hair cells may well represent convergent evolution rather than homology.

Animals↗
PubMed2004

A novel amino acid substitution is responsible for spectral tuning in a rodent violet-sensitive visual pigment.

Cone short-wave (SWS1) visual pigments can be divided into two categories that correlate with spectral sensitivity, violet sensitive above 390 nm and ultraviolet sensitive below that wavelength. The evolution and mechanism of spectral tuning of SWS1 opsins are proving more complex than those of other opsin classes. Violet-sensitive pigments probably evolved from an ancestral ultraviolet-sensitive opsin, although in birds ultraviolet sensitivity has re-evolved from violet-sensitive pigments. In certain mammals, a single substitution involving the gain of a polar residue can switch sensitivity from ultraviolet to violet sensitivity, but where such a change is not involved, several substitutions may be required to effect the switch. The guinea pig, Cavia porcellus, is a hystricognathous rodent, a distinct suborder from the Sciurognathi, such as rats and mice. It has been shown by microspectrophotometry to have two cone visual pigments at 530 and 400 nm. We have ascertained the sequence of the short-wave pigment and confirmed its violet sensitivity by expression and reconstitution of the pigment in vitro. Moreover, we have shown by site-directed mutagenesis that a single residue is responsible for wavelength tuning of spectral sensitivity, a Val86Phe causing a 60 nm short-wave shift into the ultraviolet and a Val86Tyr substitution shifting the pigment 8 nm long wave. The convergent evolution of this mammalian VS pigment provides insight into the mechanism of tuning between the violet and UV.

Amino Acid Sequence↗
PubMed2025

Tracing the evolution and genomic dynamics of mating-type loci in Cryptococcus pathogens and closely related species.

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in C. decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in K. mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

MAT genes↗
PubMed2025

The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella.

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in Cryptococcus decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in Kwoniella mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

Genes, Mating Type, Fungal↗
PubMed2002

Orientation and spatiotemporal tuning of cells in the primary visual cortex of an Australian marsupial, the wallaby Macropus eugenii.

The metatherians (marsupials) have been separated from eutherians (placentals) for approximately 135 million years. It might, therefore, be expected that significant independent evolution of the visual system has occurred. The present paper describes for the first time the orientation, direction and spatiotemporal tuning of neurons in the primary visual cortex of an Australian marsupial, the wallaby Macropus eugenii. The stimuli consisted of spatial sinusoidal gratings presented within apertures covering the classical receptive fields of the cells. The neurons can be classified as those with clear ON and OFF zones and those with less well-defined receptive field structures. Seventy-percent of the total cells encountered were strongly orientation selective (tuning functions at half height were less than 45 degrees ). The preferred orientations were evenly distributed throughout 360 degrees for cells with uniform receptive fields but biased towards the vertical and horizontal for cells with clear ON-OFF zones. Many neurons gave directional responses but only a small percentage of them (4%) showed motion opponent properties (i.e. they were excited by motion in one direction and actively inhibited by motion in the opposite direction). The median peak temporal tuning for cells with clear ON-OFF zones and those without were 3 Hz and 6 Hz, respectively. The most common peak spatial frequency tuning for the two groups were 2 cycles per degree and 0.5 cycles per degree, respectively. Spatiotemporal tuning was not always the same for preferred and antipreferred direction motion. In general, the physiology of the wallaby cortex was similar to well studied eutherian mammals suggesting either convergent evolution or a highly conserved architecture that stems from a common therian ancestor.

Animals↗
PubMed1998

Evolution of daily torpor and hibernation in birds and mammals: importance of body size.

1. The evolution of hibernation and daily torpor in mammals and birds remains a controversial subject. The original view was that use of torpor reflects a primitive thermoregulation, as it occurs in ancestral groups of mammals. 2. This view is no longer widely supported. However, the interpretation of a polyphyletic derivation of torpor also has been challenged because of the astonishing similarity of torpor patterns among various orders and even the two classes. 3. A recent argument is that mutations required for torpor and hibernation are unlikely to occur simultaneously and that torpor must be plesiomorphic (ancestral), although it is not functionally primitive. Homeothermy is interpreted as a loss of the ability to enter torpor in those groups that could survive without the requirement of heterothermic periods for energy conservation. 4. Interestingly, while torpor in mammals occurs in the phylogenetically old groups, lending support to the hypothesis of an ancestral derivation of torpor, the opposite is the case for birds. Modern bird groups and ancestral mammal groups contain mainly small species that often rely on fluctuating food supply, whereas modern mammalian orders and ancient bird orders contain the largest species with low energy requirements for maintenance and thermoregulation. 5. It is, therefore, possible that not phylogenetic position but size and diet determine the occurrence of heterothermy. Moreover, because endothermy and torpor in birds has apparently evolved separately from that in mammals and because it is possible that daily torpor and hibernation represent two distinct torpor patterns that evolved separately, a convergent evolution of torpor in endotherms cannot be excluded.

Animals↗
PubMed1998

Molecular evolution of trichromacy in primates.

Although trichromacy in Old and New World primates is based on three visual pigments with spectral peaks in the violet (SW, shortwave), green (MW, middlewave) and yellow-green (LW, longwave) regions of the spectrum, the underlying genetic mechanisms differ. The SW pigment is encoded in both cases by an autosomal gene and, in Old World primates, the MW and LW pigments by separate genes on the X chromosome. In contrast, there is a single polymorphic X-linked gene in most New World primates with three alleles coding for spectrally distinct pigments. The one reported exception to this rule is the New World howler monkey that follows the Old World system of separate LW and MW genes. A comparison of gene sequences in these different genetic systems indicates that the duplication that gave rise to the separate MW and LW genes of Old World primates is more ancient than that in the howler monkey. In addition, the amino acid sequences of the two howler monkey pigments show similarities to the pigments encoded by the polymorphic gene of other New World primates. It would appear therefore that the howler monkey gene duplication arose after the split between New and Old World primates and was generated by an unequal crossover that placed two different forms of the New World polymorphic gene on to a single chromosome. In contrast, the lack of identity at variable sites within the New and Old World systems argues for the origin of the separate genes in Old World primates by the duplication of a single form of the gene followed by divergence to give spectrally distinct LW and MW pigments. In contrast, the similarity in amino acid variation across the tri-allelic system of New World primates indicates that this polymorphism had a single origin in New World primates. A striking feature of all these pigments is the use of a common set of substitutions at three amino acid sites to achieve the spectral shift from MW at around 530 nm to LW at around 560 nm. The separate origin of the trichromacy in New and Old World primates would indicate that the selection of these three sites is the result of convergent evolution, perhaps as a consequence of visual adaptation in both cases to foraging for yellow and orange fruits against a green foliage.

Alouatta↗
PubMed1996

Stereospecificity for the hydrogen transfer and molecular evolution of pyridoxal enzymes.

We here describe the stereochemical aspects of the reactions of pyridoxal 5'-phosphate (PLP)-dependent enzymes, and the relationship between the stereochemistry of the enzyme reaction and molecular evolution of the enzyme. The reactions of PLP-dependent enzymes proceed through the formation of an anionic Schiff base intermediate between the substrate and the coenzyme. Three stereochemical possibilities exist for the formation and cleavage of bonds in the intermediate: the reaction occurs stereospecifically on either the si- or the re-face of the planar intermediate, or alternatively, non-stereospecifically on both faces. The stereospecificities for hydrogen transfer between C-4' of the cofactor and substrate in the transamination catalyzed by various PLP-dependent enzymes have been studied. The stereospecificities reflect the active-site structures of the enzymes, especially the topographical situation of a coenzyme-substrate Schiff base and a catalytic base for the hydrogen transfer. The aminotransferases and other PLP-enzymes catalyzing the transamination as a side-reaction so far studied catalyze only the si-face specific hydrogen transfer. This suggests that these PLP enzymes have similar active-site structures and are evolved divergently from a common ancestral protein. We recently established a new method for the identification of stereospecificity for the hydrogen transfer, and found that D-amino acid aminotransferase and branched chain L-amino acid aminotransferase, which have significant sequence similarity to each other, catalyze the re-face hydrogen transfer on the intermediate. The X-ray crystallographic studies of D-amino acid aminotransferase showed that the relative arrangement of the catalytic base of the enzyme active center to the C4' of the bound cofactor is opposite to that of other aminotransferases catalyzing the si-face hydrogen transfer. The folding of D-amino acid aminotransferase is also different from those of the other aminotransferase so far studied. Therefore, the classifications of the aminotransferases based on their primary structures, three dimensional structures, and stereochemistry of their hydrogen transfer coincide with one another. We also found that PLP-dependent amino acid racemases, the primary structures of which are similar to none of the other PLP-enzymes, catalyze the non-stereospecific hydrogen transfer on both faces of the planar intermediate. Stereospecificities for the hydrogen transfer suggest convergent evolution of the PLP-dependent enzymes. The stereochemical aspects of the enzyme reactions give a clue to the molecular evolution of the enzymes as well as the primary structures and three-dimensional structures of the enzymes.

Amino Acids↗
PubMed1977

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.

Animals↗
PubMed1998

Anatomical comparison of the macaque and marsupial visual cortex: common features that may reflect retention of essential cortical elements.

This study identifies fundamental anatomical features of primary visual cortex, area V1 of macaque monkey cerebral cortex, i.e., features that are present in area V1 of phylogenetically distant mammals of quite different lifestyle and features that are common to other regions of cortex. We compared anatomical constituents of macaque V1 with V1 of members of the two principal marsupial lines, the dunnart and the quokka, that diverged from the eutherian mammalian line over 135 million years ago. Features of V1 common to both macaque and marsupials were then compared with anatomical features we have previously described for macaque prefrontal cortex. Despite large differences in overall area and thickness of V1 cortex between these animals, the absolute size of pyramidal neurons is remarkably similar, as are their specific dendritic branch patterns and patterns of distribution of intrinsic axons. Pyramidal neuron patchy connections exist in the supragranular V1 in both the marsupial quokka and macaque as well as in macaque prefrontal cortex. Several specific types of aspinous interneurons are common to area V1 in both marsupial and macaque and are also present in macaque prefrontal cortex. Spiny stellate cells are a common feature of the thalamic-recipient, mid-depth lamina 4 of V1 in all three species. Because these similarities exist despite the very different lifestyles and evolutionary histories of the animals compared, this finding argues for a highly conserved framework of cellular detail in macaque primary visual cortex rather than convergent evolution of these features.

Anatomy, Artistic↗
PubMed1999

Bi-penta-bi-decaradial symmetry: A review of evolutionary and developmental trends in holothuroidea (echinodermata)

Holothuroidea, comprising the sea cucumbers, is the least studied class of extant echinoderms, yet this group possesses a wealth of features of potential interest to developmental and evolutionary biologists. Holothuroids include the most morphologically derived echinoderms, including pelagic species and spheroid, plated taxa with mouth and anus adjacent at the end of a long, flexible stalk. To begin investigating this diversity of body form, we first estimated evolutionary relationships in the class Holothuroidea based on maximum parsimony analyses of 1,075 nt of the nuclear small subunit rDNA (for six species in four orders) and on 52 informative morphological characters (for the 25 extant families). Both the morphological and molecular evidence suggests almost an inversion of the prevailing higher level classification. Character-state optimizations indicated that pronounced adult bilateral symmetry evolved three times. In one group even a regain of secondary radial symmetry is found. Respiratory trees, structures unique to holothuroids, are a relatively late innovation, are ectodermally derived, and are bilaterally symmetric, supporting the possibility that the secondary gain of bilateral symmetry in holothuroids is ectodermally derived analogous to, say, the derivation of vertebrate limb dorso-ventral axis. The test of imbricating plates found in 10% of living holothuroids is apparently not homologous with that of other heavily armored echinoderms, evolving much later and at least twice. Indirectly developing larvae, auriculariae, occur in two evolutionarily disparate clades and unlike echinoids comprise a minority of clades. We suggest that this implies the parallel convergent evolution of this larval type or, more speculatively, some form of retention of developmental constraints. J. Exp. Zool. (Mol. Dev. Evol.) 285:93-103, 1999. Copyright 1999 Wiley-Liss, Inc.

Journal Article↗
PubMed1999

Gliarin and macrolin, two novel intermediate filament proteins specifically expressed in sets and subsets of glial cells in leech central nervous system.

Using monoclonal antibodies, we have identified two novel intermediate filament (IF) proteins, Gliarin and Macrolin, which are specifically expressed in the central nervous system of an invertebrate. The two proteins both contain the coiled-coil rod domain typical of the superfamily of IF proteins flanked by unique N- and C-terminal domains. Gliarin was found in all glial cells including macro- and microglial cells, whereas Macrolin was expressed in only a single pair of giant connective glial cells. The identification of Macrolin and Gliarin together with the characterization of the strictly neuronal IF protein Filarin in leech central nervous system demonstrate that multiple neuron- and glial-specific IFs are not unique to the vertebrate nervous system but are also found in invertebrates. Interestingly, phylogenetic analysis based on maximum parsimony indicated that the presence of neuron- and glial cell-specific IFs in coelomate protostomes as well as in vertebrates is not of monophyletic origin, but rather represents convergent evolution and appears to have arisen independently.

Amino Acid Sequence↗
PubMed2000

Accurate prediction of protein functional class from sequence in the Mycobacterium tuberculosis and Escherichia coli genomes using data mining.

The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with an estimated accuracy of 60-80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, convergent evolution and horizontal gene transfer. We identify rules that predict protein functional class even in the absence of detectable sequence or structural homology. These rules give insight into the evolutionary history of M. tuberculosis and E. coli.

Amino Acid Sequence↗
PubMed1999

Homology and homoplasy: the retention of genetic programmes.

Homology describes the inevitable evolutionary phenomenon that the similarity of structures among different organisms is due to the commonality of their descent. This continuity of information is maintained in evolutionary lineages in terms of genes and developmental mechanisms and will retain 'sameness' and retard, funnel and direct evolutionary diversification. Analogous 'sameness' is said to be due to independent, convergent evolution, and also involves similarity of function; the latter is not a necessary condition for structures to be identified as homologous. Here, I suggest that the biological basis for these seemingly disparate kinds of 'sameness' in evolution may in some, or even most, instances not be all that different and may be based on the same principle-the long evolutionary retention of genes, gene interactions and developmental mechanisms. Evolution might recycle and re-recruit similar mechanisms repeatedly during its course, and it often makes do with what is already available to it rather than to newly evolve or reinvent many gene interactions and developmental mechanisms repeatedly. Apparently there is no, or only a negligible, 'genomic cost' or even a selective advantage to maintaining genes and developmental mechanisms for long evolutionary periods of time, even if they are not continuously used in all members along an evolutionary line. Therefore, the biological basis of both homologous traits (those that are evolutionarily always expressed) and homoplasious traits (those that are not always 'on', but are 're-awakened' during evolution) might not be so different, and the distinction between homology and some forms of homoplasy may be somewhat artificial.

Amphibians↗
PubMed1989

Scanning and transmission electron microscopic study of the tracheal air sac system in a grasshopper Chrotogonus senegalensis (Kraus)--Orthoptera: Acrididae: Pyrgomorphinae.

The morphology of the trachea-air sac system in a species of grasshopper Chrotogonus senegalensis has been studied by using scanning and transmission electron microscopes. Capacious air sacs were formed as dilatations along the primary tracheal trunks. Narrower secondary trachea arose either directly from the primary trachea that bypassed the air sacs or from the air sacs themselves. At or close to the organ or tissue supplied with air, the secondary trachea gave rise to the notably smaller tertiary trachea that penetrated the tissue, giving rise terminally to the extremely small tracheoles that indent some cells. The trachea and the air sacs were basically made up of an inner cuticular lining, helical taenidial rings, and an overlying epithelial cell cover. The air sacs may be important in efficient ventilation of the respiratory system. The supply of air directly to the tissue cells was viewed as an exemplary efficient design when compared to that prevailing in the nontracheate air-breathing animals, where the vascular system is interposed between the respiratory organ and the target tissue cells. A similarity in the general morphological design of the insect and avian respiratory systems has been observed, mainly in respect to the presence of the air sacs and that of the respiratory shunts. This, together with the reported functional features like the unidirectional mode of ventilation, has been interpreted as a classic case of structural and functional convergent evolution leading to the evolution of similar and comparably efficient respiratory systems capable of providing the large amount of oxygen demanded by flight.

Air Sacs↗