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PubMed2001

Molecular and functional evidence for early divergence of an endothelin-like system during metazoan evolution: analysis of the Cnidarian, hydra.

A novel putative endothelin-converting enzyme (ECE) has been cloned from hydra, a freshwater invertebrate that belongs to the second oldest phylum of the animal kingdom. As an integral component of the endothelin system, vertebrate ECE functions in the activation of endothelin (ET) peptides. Vertebrate ETs are (1) the most potent vasoconstrictors known in mammals; and (2) function as essential signaling ligands during development of tissues derived from neural crest cells. To date, only a limited number of immunocytochemical studies have suggested the presence of endothelin-like peptides in invertebrates. Based on structural and functional analyses, we present evidence for a functional endothelin-like system in hydra that is involved in both muscle contraction and developmental processes. These findings indicate the broad use of endothelin systems in metazoans and also indicate that this type of signaling system arose early in evolution even before divergence of protostomes and deuterostomes.

Amino Acid Sequence↗
PubMed2003

Functional divergence in protein (family) sequence evolution.

As widely used today to infer 'function', the homology search is based on the neutral theory that sites of greatest functional significance are under the strongest selective constraints as well as lowest evolutionary rates, and vice versa. Therefore, site-specific rate changes (or altered selective constraints) are related to functional divergence during protein (family) evolution. In this paper, we review our recent work about this issue. We show a great deal of functional information can be obtained from the evolutionary perspective, which can in turn be used to facilitate high throughput functional assays. The emergence of evolutionary functional genomics is also indicated. The related software DIVERGE can be obtained from http://xgu1.zool.iastate.edu.

Amino Acid Sequence↗
PubMed1990

Sulfobacillus thermosulfidooxidans: a new lineage of bacterial evolution?

The nucleotide sequence of 5 S ribosomal RNA (rRNA) of type strain Sulfobacillus thermosulfidooxidans VKM B-1269 was determined. This organism represents a group of moderately thermophilic acidophilic chemolithotrophic bacteria, able to use ferrous and sulfur compounds as the sole energy source. 5 S rRNA of this bacterium is drastically different from all other known bacterial 5 S rRNA sequences. It is suggested that S. thermosulfidooxidans represents a new lineage of bacterial evolution, that diverged from other bacteria at an early step of their evolution.

Base Sequence↗
PubMed2005

Evolution of flavors and scents.

The world is filled with flavors and scents, which are the result of volatile compounds produced and emitted by plants. These specialized metabolites are the products of specific metabolic pathways. The terpenoid, fatty acid, and phenylpropanoid pathways contribute greatly to production of volatile compounds. Mechanisms that lead to evolution of volatile production in plants include gene duplication and divergence, convergent evolution, repeated evolution, and alteration of gene expression, caused by a number of factors, followed by change in enzyme specificity. Many examples of these processes are now available for three important gene families involved in production of volatile metabolites: the small molecule O-methyltransferases, the acyltransferases, and the terpene synthases. Examples of these processes in these gene families are found in roses, Clarkia breweri, and sweet basil, among others. Finally, evolution of volatile emission will be an exciting field of study for the foreseeable future.

Biological Evolution↗
PubMed1998

Positive selection driving the evolution of a gene of male reproduction, Acp26Aa, of Drosophila: II. Divergence versus polymorphism.

The evolution of the gene for a male ejaculatory protein, Acp26Aa, has been shown to be driven by positive selection when nonsibling species in the Drosophila melanogaster subgroup are compared. To know if selection has been operating in the recent past and to understand the details of its dynamics, we obtained DNA sequences of Acp26Aa and the nearby Acp26Ab gene from 39 D. melanogaster chromosomes. Together with the 10 published sequences, we analyzed 49 sequences from five populations in four continents. The southern African population is somewhat differentiated from all other populations, but its nucleotide diversity is lower at these two loci. We find the following results for Acp26Aa: (1) The R: S (replacement : silent changes) ratio is significantly higher in the between-species comparisons than in the within-species data by the McDonald and Kreitman test. Positive selection is probably responsible for the excess of amino acid replacements between species. (2) However, within-species nucleotide diversity is high. Neither the Tajima test nor the Fu and Li test indicates a reduction in nucleotide diversity due to positive selection in the recent past. (3) The newly derived nucleotides in D. melanogaster are at high frequency significantly more often than predicted by the neutral equilibrium. Since the nearby Acp26Ab gene does not show these patterns, these observations cannot be attributed to the characteristics of this chromosomal region. We suggest that positive selection is active, but may be weak, for each amino acid change in the Acp26Aa gene.

Animals↗
PubMed1991

phyB is evolutionarily conserved and constitutively expressed in rice seedling shoots.

Southern blot analysis indicates that the rice genome contains single copies of genes encoding type A (phyA) and type B (phyB) phytochromes. We have isolated overlapping cDNA and genomic clones encoding the entire phyB polypeptide. This monocot sequence is more closely related to phyB from the dicot, Arabidopsis (73% amino acid sequence identity), than it is to the phyA gene in the rice genome (50% identity). These data support the proposal that phyA and phyB subfamilies diverged early in plant evolution and that subsequent divergence accompanied the evolution of monocots and dicots. Moreover, since rice and Arabidopsis phyB polypeptides are more closely related to one another (73% identity) than are monocot and dicot phyA sequences (63-65% identity), it appears that phyB has evolved more slowly than phyA. Sequence conservation between phyA and phyB is greatest in a central core region surrounding the chromophore attachment site, and least toward the amino-terminal and carboxy-terminal ends of the polypeptides, although hydropathy analysis suggests that the overall structure of the two phytochromes has been conserved. Gene-specific Northern blot analysis indicates that, whereas phyA is negatively regulated by phytochrome in rice seedling shoots in the manner typical of monocots, phyB is constitutively expressed irrespective of light treatment. In consequence, phyA and phyB transcripts are equally abundant in fully green tissue. Since Arabidopsis phyB mRNA levels are also unaffected by light, the present results suggest that this mode of regulation is evolutionarily conserved among phyB genes, perhaps reflecting differences in the functional roles of the different phytochrome subfamilies.

Amino Acid Sequence↗
PubMed2005

Allopatric origins of sympatric brook charr populations: colonization history and admixture.

Natural selection is presumed to be the driving force behind the occurrence of phenotypically and genetically divergent populations in sympatry within many north temperate freshwater fishes. If, however, these populations have different ancestral origins, history could also contribute to their divergence. We previously found evidence for the role of selection in the evolution of divergent outflow and inflow breeding populations of migratory brook charr (Salvelinus fontinalis) inhabiting postglacial Mistassini Lake (Quebec, Canada). Here, we show that these populations do not have a common origin, through the use of admixture and spatial analyses with seven microsatellite loci. Divergent populations clustered into two different population groups when compared to samples from surrounding drainages, although inflow populations appeared to be more admixed between the two population groups than the outflow population. These results are noteworthy since outflow and inflow populations were monomorphic at mitochondrial DNA (338-bp sequence of the control region) and are only moderately differentiated (mean F(ST) = 0.10). Colonization by two ancestral populations was also consistent with known outflow direction changes throughout lake formation. In addition to providing insight into how phenotypic divergence in sympatry may have been affected by the nature (i.e. timing and direction) of colonization of ancestral populations, our results also suggest that ancestral populations may have differed in their ability to colonize certain lake habitats.

Animals↗
PubMed2006

Evolutionary conservation of protein backbone flexibility.

Internal protein dynamics is essential for biological function. During evolution, protein divergence is functionally constrained: properties more relevant for function vary more slowly than less important properties. Thus, if protein dynamics is relevant for function, it should be evolutionary conserved. In contrast with the well-studied evolution of protein structure, the evolutionary divergence of protein dynamics has not been addressed systematically before, apart from a few case studies. X-Ray diffraction analysis gives information not only on protein structure but also on B-factors, which characterize the flexibility that results from protein dynamics. Here we study the evolutionary divergence of protein backbone dynamics by comparing the C(alpha) flexibility (B-factor) profiles for a large dataset of homologous proteins classified into families and superfamilies. We show that C(alpha) flexibility profiles diverge slowly, so that they are conserved at family and superfamily levels, even for pairs of proteins with nonsignificant sequence similarity. We also analyze and discuss the correlations among the divergences of flexibility, sequence, and structure.

Amino Acid Sequence↗
PubMed2002

Kinesin-related genes from diplomonad, sponge, amphioxus, and cyclostomes: divergence pattern of kinesin family and evolution of giardial membrane-bounded organella.

To understand the question of whether divergence of eukaryotic genes by gene duplications and domain shufflings proceeded gradually or intermittently during evolution, we have cloned and sequenced Giardia lamblia cDNAs encoding kinesins and kinesin-related proteins and have obtained 13 kinesin-related cDNAs, some of which are likely homologs of vertebrate kinesins involved in vesicle transfer to ER, Golgi, and plasma membrane. A phylogenetic tree of the kinesin family revealed that most gene duplications that gave rise to different kinesin subfamilies with distinct functions have been completed before the earliest divergence of extant eukaryotes. This suggests that the complex endomembrane system has arisen very early in eukaryotic evolution, and the diminutive ER and Golgi apparatus recognized in the giardial cells, together with the absence of mitochondria, might be characters acquired secondarily during the evolution of parasitism. To understand the divergence pattern of the kinesin family in the lineage leading to vertebrates, seven more Unc104-related cDNAs have been cloned from sponge, amphioxus, hagfish, and lamprey. The divergence pattern of the animal Unc104/KIF1 subfamily is characterized by two active periods in gene duplication interrupted by a considerably long period of silence, instead of proceeding gradually: animals underwent extensive gene duplications before the parazoan-eumetazoan split. In the early evolution of vertebrates around the cyclostome-gnathostome split, further gene duplications occurred, by which a variety of genes with similar structures over the entire regions were generated. This pattern of divergence is similar to those of animal genes involved in cell-cell communication and developmental control.

Animals↗
PubMed1998

Somatic and dendritic mosaics formed by large ganglion cells in the retina of the common house gecko (Hemidactylus frenatus).

Recent studies of large ganglion cells in fishes and frogs have identified a shared inventory of three basic types, with characteristic forms and spatially independent mosaic distributions. These anamniote types and mosaics are hard to match to the large ganglion cell types and mosaics of mammals, implying that the underlying developmental programmes have diverged during evolution. Reptiles and mammals both belong to the amniote lineage, so the point of divergence can be investigated by comparing the large ganglion cells of reptiles with those of mammals, taking fishes and frogs as outgroups. With this aim, ganglion cells of the common house gecko, Hemidactylus frenatus, were labelled with horse-radish peroxidase by an in vitro method and studied in retinal flatmounts. Two prominent, regular, spatially independent mosaics were consistently present. One (alpha a) was characterized by somata displaced into the inner nuclear layer and dendrites forming planar trees in sublamina a; the other (alpha ab) comprised large orthotopic somata and distinctive, bistratified dendrites that formed discrete planar subtrees in sublaminae a and b. These subtrees were joined by up to 40 vertical link segments, whose distribution was found to correlate with the underlying photoreceptor mosaic. Some specimens also contained patches of a third mosaic (alpha c), characterized by large orthotopic somata and very large flat trees in sublamina c, but the labelling of this type was inconsistent. These reptilian mosaics share several distinctive characters with anamniote alpha-cell mosaics but differ markedly from the ganglion cell mosaics of any known mammal. The most parsimonious conclusion is that those mosaic features that are shared by the ganglion cells of all nonmammals are homologous and primitive (symplesiomorphic), while those that are shared by all therian mammals are homologous and derived (synapomorphic). This is consistent with other differences between mammalian and nonmammalian eyes. Mosaic formation itself, however, seems to be a universal characteristic of large ganglion cells.

Animals↗
PubMed1984

Duplicated immunoglobulin gamma 2a genes in wild mice.

The Japanese wild mouse, Mus musculus molossinus, has duplicated immunoglobulin gamma 2a genes, whereas most of the laboratory-strain mice have single gamma 2a genes. This duplication provides a unique system in which molecular mechanisms of the evolutionary rearrangement of the immunoglobulin gene can be studied. For this purpose it is important to elucidate the organization of the immunoglobulin genes surrounding the duplicated gamma 2a genes. It is also interesting to assess the distribution of this haplotype among the wild mouse population. Partially overlapping chromosomal segments that encompass the gamma 2b, gamma 2a-1, gamma 2a-2, and epsilon genes were isolated from phage libraries containing DNA fragments from M. m, molossinus. The organization of this region has been elucidated as 5'-gamma 2b-(18 kb)-gamma 2a-1-(19 kb)-gamma 2a-2-(14 kb)-epsilon-3'. Both gamma 2a-1 and gamma 2a-2 genes have their own switch regions in the 5' flanking region. Two homology units of 13 kb, each containing the gamma 2a gene, were identified. The homology units alternate with repetitive sequences of low homology, making the location of the recombination site obscure. Seventeen of 31 Japanese and Chinese wild mice screened had duplicated gamma 2a genes, indicating a wide distribution of this genetic event in the Asian wild mouse population. Moreover, three alleles each of the gamma 2b and gamma 2a loci have been observed in this small sample population. An unequal crossing-over event between heterologous haplotypes is proposed to account for the duplication of the gamma 2a gene, and a candidate for one member of the pair was identified among wild mouse haplotypes. These results suggest that the immunoglobulin heavy-chain gene family of the Japanese and Chinese wild mouse subspecies has accumulated not only polymorphic divergence due to point mutations, but also dynamic rearrangements such as gene duplication, during its recent evolution since divergence of these subspecies from the European subspecies about one million years ago.

Animals↗
PubMed2004

Divergence in replicated phylogenies: the evolution of partial post-mating prezygotic isolation in bean weevils.

By tradition, speciation research has been focused on processes leading to either premating or post-zygotic reproductive isolation. The processes which generate isolation after mating but before zygote formation are less well understood. Here, we study divergence in characters which contribute to post-mating prezygotic isolation, such as egg production and remating rate. We propose that 'replicated' laboratory phylogenies with known histories can be used to yield insights into the processes of divergence. We performed a series of cross-matings between populations within two strains of the bean weevil Callosobruchus maculatus. Each strain has a unique and independent origin and both have been kept in the same set of laboratories during the last few decades. Our results show that divergence has occurred between laboratory populations within strains with regards to the effects that mating has on female reproductive behaviour, showing that the evolution of partial post-mating prezygotic isolation can be rapid. More importantly, the pattern of divergence across populations was distinct in the two strains, suggesting that coevolutionary trajectories are not determined by environmental factors but are to some extent arbitrary. We discuss the limitations of the novel empirical strategy employed here, and conclude that our results lend support to the hypothesis that post-mating sexual selection is capable of rapidly generating post-mating prezygotic isolation.

Animals↗
PubMed1998

Placental endogenous retrovirus (ERV): structural, functional, and evolutionary significance.

That endogenous retrovirus (ERV) is present within the placenta of humans and other mammals has been known for the past 25 years, but the significance of this observation is still not fully understood. Much molecular biological data have emerged in recent years to support the earlier electron microscopic data on the presence of placental ERV. The evidence for ERV in animal and human placental tissue is presented, then integrated with data on the presence of ERV in a range of other tissues, in particular teratocarcinoma cells. Placental invasiveness and maternal immunosuppression are then discussed in relation to metalloproteinase secretion, the immunosuppressive potential of retroviruses, and placental growth factors, while the evidence for a functional link between placental protooncogenes and trophoblast malignancy is reviewed. Finally, placental development, structure, and life span are discussed within an evolutionary context. The hypothesis that one or more ancient trophoblastic ERVs could have played a role in the evolution and divergence of all placental mammals is evaluated.

Animals↗
PubMed1979

Analysis of the constancy of DNA sequences during development and evolution of the nematode Caenorhabditis elegans.

In order to test for the occurrence of rearrangements in DNA during development and to assess the rate of DNA divergence during evolution, we have compared restriction fragments derived from DNA from four sources: sperm cells and somatic tissues of one strain of the nematode Caenorhabditis elegans, somatic tissues of a second strain of the same species, and whole animals of a closely related species. Restriction fragments were detected by hybridizing radioactive cloned fragments to restriction digests that had been fractionated by size on agarose gels and transferred to nitrocellulose sheets. In this way, approximately 50 BamHI restriction fragments were visualized and compared. Fragments from sperm and somatic DNAs were found to be identical; 15% differed in size between the two strains. Little cross homology was found between the two species. We conclude that, if rearrangements occur in C. elegans DNA during development, they must affect fewer than a few percent of the restriction fragments or restriction sites. The difference found between the two strains and the two species is surprisingly great.

Animals↗
PubMed2005

The evolution of male genitalia: patterns of genetic variation and covariation in the genital sclerites of the dung beetle Onthophagus taurus.

Three main hypotheses, have been invoked to explain divergent genital evolution, the lock and key, pleiotropy, and sexual selection hypotheses, each of which make different predictions about how genital traits are inherited. Here we used a half-sib breeding design to examine the patterns of genetic variation and covariation between male genital sclerites, and their covariance with general body morphology in the dung beetle Onthophagus taurus. We found CV(A)'s and CV(P)'s were similar for both genital and general morphological traits and that CV(R)'s were large for both trait types. We found that male genital sclerites were negatively genetically correlated with general morphological traits. Variation in male genital morphology has direct implications for a male's fertilization success and the resulting sexual selection acting on male genitalia is predicted to maintain high levels of additive genetic variance. Contrary to this prediction, we found that individual genital sclerites all had low levels of additive genetic variance and large maternal and environmental sources of variation. Our data suggest that the genital sclerites in O. taurus are not inherited independently but as a genetically integrated unit. More importantly, the way the different sclerites function to influence male fertilization success reflects this genetic integration. Even though levels of V(A) in individual genital sclerites may be low, there may still be sufficient V(A) in multivariate trait space for selection to generate evolutionary change in the overall morphology of male genitalia.

Animals↗
PubMed1999

The discovery of two new divergent STLVs has implications for the evolution and epidemiology of HTLVs.

We have isolated and characterised two divergent simian T-lymphotropic viruses (STLV), not belonging to the established human and simian T-lymphotropic virus lineages HTLV-1/STLV-1 and HTLV-2. STLV-L, from an Eritrean sacred baboon (Papio hamadryas), has been typed as a third type of simian T-lymphotropic virus, distinct from HTLV-1/STLV-1 and HTLV-2. The other virus, isolated from Congolese bonobos (Pan paniscus), is a distinct member of the HTLV-2 clade and has been designated STLV-2. The isolation of these two simian viruses shows that the spectrum of HTLVs/STLVs is larger than previously expected. Our data indicate that the two lineages STLV-L and HTLV-2/STLV-2 are of African origin, while the HTLV-1/STLV-1 lineage has been shown to be of Asian origin. These data, together with our phylogenetic analyses, suggest an African origin of the HTLV/STLV ancestor, which provides new clues about virus dissemination. Furthermore, the atypical serological profiles exhibited by STLV-L or STLV-2 infected animals in western blot, raise questions about the efficiency of current screening methods to type highly divergent HTLVs/STLVs. Considering the growing interest in xenotransplantations, more epidemiological and biological knowledge of simian and human T-lymphotropic viruses is necessary to estimate the risk of interspecies transmissions.

Animals↗
PubMed1999

Protein evolution and protein folding: non-functional conserved residues and their probable role.

It is shown that there are two types of conserved residues in evolutionary and functionally related proteins whose sequences have been well diverged in evolution. The first group consists of residues forming the active center, while the second (first established in this work) has nothing to do with function and therefore should be related to protein structure and/or protein folding. The lattter group consists of 4 residues in c-type cytochromes and 6 residues in globins. All these residues belong to alpha-helices and occupy positions (i, i + 4) or (i, i + 3), stabilizing one helical turn in some helices. These residues form an interface between the N- and C-terminal helices in c-type cytochromes and helices A, G, H in globins. These helical complexes form early in protein folding and are relatively stable in both equilibrium and kinetic folding intermediates. The attractive hypothesis is that these helices form folding nuclei in protein in the frame of the nucleation-growth mechanism of protein folding.

Amino Acid Sequence↗