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PubMed2001

Convergence and divergence in the evolution of aquatic birds.

Aquatic birds exceed other terrestrial vertebrates in the diversity of their adaptations to aquatic niches. For many species this has created difficulty in understanding their evolutionary origin and, in particular, for the flamingos, hamerkop, shoebill and pelecaniforms. Here, new evidence from nuclear and mitochondrial DNA sequences and DNA-DNA hybridization data indicates extensive morphological convergence and divergence in aquatic birds. Among the unexpected findings is a grouping of flamingos and grebes, species which otherwise show no resemblance. These results suggest that the traditional characters used to unite certain aquatic groups, such as totipalmate feet, foot-propelled diving and long legs, evolved more than once and that organismal change in aquatic birds has proceeded at a faster pace than previously recognized.

Animals↗
PubMed2004

[Divergence and systematical evolution of three Leuciscus species in Xinjiang based on mitochondrial DNA control region sequences].

Nucleotide sequence of fish mitochondria DNA (mtDNA) D-loop region from Leuciscus leuciscus baicalensis, L. merzbacheri, and L. idus in Xinjiang, China, were examined by sequencing 667 - 669 bp length of homological fragments in the D-loop from 24 individuals of the three fish species. DNA divergence ranged from 6.39% - 9.89% among the three fish species in the genius of Leuciscus cuvier. The sequence similarity is high and the variation is low between L. Leuciscus baicalensis and L. idus. In contract, the genetic distance is larger between L. Leuciscus baicalensis and L. merzbacheri. The average nucleotide variation within each of the two geographical populations (Sailimu lake and E' erqis river) of L. leuciscus baicalensis is 1.07% and 1.08%, respectively, and such variation is 1.07% between the two populations. These results demonstrate that the two geographic populations of L. leuciscus baicalensis do not appear to have significant genetic differentiation. Sequencing data showed the existence of sufficient genetic variations among three species of fish, as illustrated by distinct haplotypes for each species. The phylogenetic trees built with MEGA1.02 pointed out that the relationship between L. leuciscus baicalensis and L. idus is close, and L. merzbacheri is ancient among three Leuciscus.

Animals↗
PubMed1987

Recruitment of lysozyme as a major enzyme in the mouse gut: duplication, divergence, and regulatory evolution.

Two major types of lysozyme c (M and P) occur in the mouse genus, Mus, and have been purified from an inbred laboratory strain (C58/J) of M. domesticus. They differ in physical, catalytic, and antigenic properties as well as by amino acid replacements at 6 of 49 positions in the amino-terminal sequence. Comparisons with four other mammalian lysozymes c of known sequence suggest that M and P are related by a gene duplication that took place before the divergence of the rat and mouse lineages. M lysozyme is present in most tissues; achieves its highest concentration in the kidney, lung, and spleen; and corresponds to the lysozyme partially sequenced before from another strain of M. domesticus. In M. domesticus and several related species, P lysozyme was detected chiefly in the small intestine, where it is probably produced mainly by Paneth cells. A survey of M and P levels in 22 species of muroid rodents (from Mus and six other genera) of known phylogenetic relationships suggests that a mutation that derepressed the P enzyme arose about 4 million years ago in the ancestor of the housemouse group of species. Additional regulatory shifts affecting M and P levels have taken place along lineages leading to other muroid species. Our survey of 187 individuals of wild house mice and their closest allies reveals a correlation between latitude of origin and level of intestinal lysozyme.

Amino Acid Sequence↗
PubMed2003

Gene duplications: the gradual evolution of functional divergence.

Budding yeast provides a useful resource for studies of gene function. A new analysis of the fitness effects of deletion mutations in budding yeast reveals that genes that have duplicates create lower fitness losses when inactivated than do genes that are singletons.

Animals↗
PubMed2002

Predicting functional divergence in protein evolution by site-specific rate shifts.

Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.

Amino Acid Sequence↗
PubMed2001

Maximum-likelihood approach for gene family evolution under functional divergence.

According to the observed alignment pattern (i.e., amino acid configuration), we studied two basic types of functional divergence of a protein family. Type I functional divergence after gene duplication results in altered functional constraints (i.e., different evolutionary rate) between duplicate genes, whereas type II results in no altered functional constraints but radical change in amino acid property between them (e.g., charge, hydrophobicity, etc.). Two statistical approaches, i.e., the subtree likelihood and the whole-tree likelihood, were developed for estimating the coefficients of (type I or type II) functional divergence. Numerical algorithms for obtaining maximum-likelihood estimates are also provided. Moreover, a posterior-based site-specific profile is implemented to predict critical amino acid residues that are responsible for type I and/or type II functional divergence after gene duplication. We compared the current likelihood with a fast method developed previously by examples; both show similar results. For handling altered functional constraints (type I functional divergence) in the large gene family with many member genes (clusters), which appears to be a normal case in postgenomics, the subtree likelihood provides a solution that is computationally feasible and robust against the uncertainty of the phylogeny. The cost of this feasibility is the approximation when frequencies of amino acids are very skewed. The potential bias and correction are discussed.

Amino Acid Sequence↗
PubMed2005

Electrophysiological properties of neurons in the basal ganglia of the domestic chick: conservation and divergence in the evolution of the avian basal ganglia.

Although the basal ganglia of birds and mammals share an enormous number of anatomical, histochemical, and electrophysiological characteristics, studies in songbirds have revealed some important differences. Specifically, a specialized region of songbird striatum (the input structure of the basal ganglia) has an anatomical projection and a physiologically defined cell type that are characteristic of the globus pallidus. At present, it is not clear if these differences result from adaptations specific to songbirds and perhaps a few other avian taxa or are common to all birds. We shed some light on this issue by characterizing the morphology and electrophysiological properties of basal ganglia neurons in an avian species that is only distantly related to songbirds: the domestic chick. We recorded neurons in chick basal ganglia in a brain slice preparation, using the whole cell technique. We found that chick striatum, like songbird striatum, contains a pallidum-like cell type never reported in mammalian striatum, supporting the hypothesis that this feature is common to all birds. We also discovered that spiny neurons, the most common cell type in the striatum of all amniotes, possess a diverse set of physiological properties in chicks that distinguish them from both mammals and songbirds. This study revealed an unexpectedly complex pattern of conservation and divergence in the properties of neurons recorded in avian striatum.

Age Factors↗
PubMed2004

AdoMet radical proteins--from structure to evolution--alignment of divergent protein sequences reveals strong secondary structure element conservation.

Eighteen subclasses of S-adenosyl-l-methionine (AdoMet) radical proteins have been aligned in the first bioinformatics study of the AdoMet radical superfamily to utilize crystallographic information. The recently resolved X-ray structure of biotin synthase (BioB) was used to guide the multiple sequence alignment, and the recently resolved X-ray structure of coproporphyrinogen III oxidase (HemN) was used as the control. Despite the low 9% sequence identity between BioB and HemN, the multiple sequence alignment correctly predicted all but one of the core helices in HemN, and correctly predicted the residues in the enzyme active site. This alignment further suggests that the AdoMet radical proteins may have evolved from half-barrel structures (alphabeta)4 to three-quarter-barrel structures (alphabeta)6 to full-barrel structures (alphabeta)8. It predicts that anaerobic ribonucleotide reductase (RNR) activase, an ancient enzyme that, it has been suggested, serves as a link between the RNA and DNA worlds, will have a half-barrel structure, whereas the three-quarter barrel, exemplified by HemN, will be the most common architecture for AdoMet radical enzymes, and fewer members of the superfamily will join BioB in using a complete (alphabeta)8 TIM-barrel fold to perform radical chemistry. These differences in barrel architecture also explain how AdoMet radical enzymes can act on substrates that range in size from 10 atoms to 608 residue proteins.

Amino Acid Sequence↗
PubMed1993

Evolution of sequence divergence among human immunodeficiency virus type 1 isolates derived from a blood donor and a recipient.

Four neonates who were infected with a single unit of blood from a human immunodeficiency virus-1 (HIV-1)-infected adult (patient 1) were studied. Two of the infected children (patients II and III) developed symptomatic HIV-1 disease and died within the first 3 y of life. One child (patient IV) died at 8 mo of age of clinical problems that may have been HIV-related. In contrast, one child (patient V) has remained asymptomatic for 7.5 y and has exhibited a very gradual decline in CD4+ cell number. A previous study had shown very limited sequence diversity of isolates from patients I, II, and III (McNearney T et al.: Proc Natl Acad Sci USA 87:1917-1921, 1990). The current study examined additional HIV-1 sequences encoding the principal neutralizing V3 loop of the surface envelope protein of isolates from patients I and V. Amplified sequences were obtained using the polymerase chain reaction from a cultured isolate and uncultured peripheral blood leukocytes, and nucleotide sequences were determined for 13 clones from patient I and 19 clones from patient V. Clones derived from the cultured isolate exhibited less predicted amino acid sequence diversity on average (0-5.2%) than did sequences from uncultured leukocytes (0-19.8% differences). All clones were more closely related to those from patients II and III (0-19.8% amino acid differences) than to other North American or European isolates (18.8-27.0% amino acid differences) or African isolates (41.0-48.0% amino acid differences). Substitutions occurred at sites predicted to modulate host cell tropism and proteolytic cleavage of the V3 loop.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1994

Sequence divergence, polymorphism and evolution of the middle-wave and long-wave visual pigment genes of great apes and Old World monkeys.

In man, the spectral shift between the middle-wave (MW) and long-wave (LW) visual pigments is largely achieved by amino acid substitution at two codons, both located in exon 5. A third amino acid site coded by exon 3 is polymorphic between pigments. We have studied the equivalent regions of the cone opsin genes in two members of the Hominidea (the gorilla, Gorilla gorilla and the chimpanzee, Pan troglodytes) and in three members of the Cercopithecoidea family of Old World primates (the diana monkey, Cercopithecus diana, the talapoin monkey, Miopithecus talapoin, and the crab-eating macaque, Macaca fascicularis). No variation in the codons that specify the amino acids involved in spectral tuning were found. We predict therefore that the MW and LW pigments of gorilla and chimpanzee have similar spectral characteristics to those of man. Multiple copies of the same opsin gene sequence were identified in the chimpanzee, talapoin and macaque and we also show that non-human Old World primates are similar to man in showing a bunching of polymorphic sites in exon 3. We discuss the ancestry of the separate MW and LW genes of Old World primates and the equivalent polymorphic gene of the marmoset, a New World primate.

Amino Acid Sequence↗
PubMed1998

Ribonuclease k6: chromosomal mapping and divergent rates of evolution within the RNase A gene superfamily.

We have localized the gene encoding human RNase k6 to within approximately 120 kb on the long (q) arm of chromosome 14 by HAPPY mapping. With this information, the relative positions of the six human RNase A ribonucleases that have been mapped to this locus can be inferred. To further our understanding of the individual lineages comprising the RNase A superfamily, we have isolated and characterized 10 novel genes orthologous to that encoding human RNase k6 from Great Ape, Old World, and New World monkey genomes. Each gene encodes a complete ORF with no less than 86% amino acid sequence identity to human RNase k6 with the eight cysteines and catalytic histidines (H15 and H123) and lysine (K38) typically observed among members of the RNase A superfamily. Interesting trends include an unusually low number of synonymous substitutions (Ks) observed among the New World monkey RNase k6 genes. When considering nonsilent mutations, RNase k6 is a relatively stable lineage, with a nonsynonymous substitution rate of 0.40 x 10(-9) nonsynonymous substitutions/nonsynonymous site/year (ns/ns/yr). These results stand in contrast to those determined for the primate orthologs of the two closely related ribonucleases, the eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP), which have incorporated nonsilent mutations at very rapid rates (1.9 x 10(-9) and 2.0 x 10(-9) ns/ns/yr, respectively). The uneventful trends observed for RNase k6 serve to spotlight the unique nature of EDN and ECP and the unusual evolutionary constraints to which these two ribonuclease genes must be responding. [The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF037081-AF037090.]

Amino Acid Sequence↗
PubMed1990

Two divergent routes of evolution gave rise to the DRw13 haplotypes.

The HLA class II genes and haplotypes have evolved over a long period of evolutionary time by mechanisms such as gene conversion, reciprocal recombination and point mutation. The extent of the diversity generated is most clearly evident in an analysis of the HLA class II alleles present within DRw13 haplotypes. This study uses cDNA sequencing to examine the first domains of DRB1, DRB3, DQA1, and DQB1 alleles from several American black individuals expressing seven different DRw13 haplotypes, five with undefined HLA-D specificities (i.e., not Dw18 or Dw19). Two new DRw13 alleles described in this study are the first examples of convergent evolution of DR alleles in which gene conversion has apparently combined segments of DRB1 alleles encoding DRw11 and DRw8 to generate two new DRB1 alleles, DRB1*1303 and DRB1*1304, that encode molecules bearing serologic determinants of a third allele, DRw13. These new DRw13 alleles are found embedded in haplotypes of DRw11 origin distinct from haplotypes encoding previously identified DRw13 alleles, DRB1*1301 and DRB1*1302. These data suggest that two evolutionary pathways may have given rise to two subgroups of alleles encoding molecules that share DRw13 serologic determinants yet which possess different structural and, likely, functional motifs. Reciprocal gene recombination events resulting in different DR, DRw52 and DQ allele combinations also appear to have played a crucial role in augmenting the level of diversity found in DRw13 haplotypes. Recombination has resulted in the association of one of the new DRw13 alleles with a DQw2 allele normally found associated with DR7 and the association of the DRw52c-associated DRw13 allele (DRB1*1302) with three different DQw1 alleles. The seven DRw13 haplotypes that have resulted from the effect of recombination on haplotypes formed by the two pathways of DRw13 allelic diversification have resulted in different repertoires of class II molecules and, most likely, different immune response profiles in individuals with these haplotypes.

Alleles↗
PubMed2003

Ribosomal DNA variation, recombination and inheritance in the basidiomycete Trichaptum abietinum: implications for reticulate evolution.

Two divergent nuclear ribosomal DNA (nrDNA) types, designated alpha and beta, were found distributed in 11 North European populations of the basidiomycete Trichaptum abietinum. These types differed by a 220 bp indel in the internal transcribed spacer 1 (ITS1) sequence and a number of linked substitutions and small indel motives in the internal transcribed and intergenic spacers (ITS1, ITS2, IGS1 and IGS2). The alpha and beta haplotypes co-occurred in heterozygous somatic individuals (dikaryons) and segregated in a Mendelian fashion in monokaryotic single spore progenies. This result suggests that the haplotypes are encoded in different nuclei of field-collected dikaryons and inherited as a single locus. No meiotic recombinants were observed among the sequenced monokaryons. Population genetic analyses by PCR-RFLP revealed that a low frequency of evolutionary intermediate nrDNA types also existed in natural populations, presumably as a result of meiotic recombination of alpha and beta nrDNA. The existence of divergent nrDNA types in T. abietinum could be a result of a former independent evolution followed by a hybridization event. Phylogenetic analyses of ITS sequences suggest that the sister taxon T. fusco-violaceum has been involved in the evolutionary history of T. abietinum. Sequence polymorphisms observed in the translation elongation factor 1alpha (efa) and glyceraldehyde-3-phosphate dehydrogenase (gpd) genes, did not reveal two well-defined types of these genes. The results are discussed in the light of other evolutionary mechanisms as well.

DNA, Fungal↗
PubMed2005

Divergent selection and the evolution of signal traits and mating preferences.

Mating preferences are common in natural populations, and their divergence among populations is considered an important source of reproductive isolation during speciation. Although mechanisms for the divergence of mating preferences have received substantial theoretical treatment, complementary experimental tests are lacking. We conducted a laboratory evolution experiment, using the fruit fly Drosophila serrata, to explore the role of divergent selection between environments in the evolution of female mating preferences. Replicate populations of D. serrata were derived from a common ancestor and propagated in one of three resource environments: two novel environments and the ancestral laboratory environment. Adaptation to both novel environments involved changes in cuticular hydrocarbons, traits that predict mating success in these populations. Furthermore, female mating preferences for these cuticular hydrocarbons also diverged among populations. A component of this divergence occurred among treatment environments, accounting for at least 17.4% of the among-population divergence in linear mating preferences and 17.2% of the among-population divergence in nonlinear mating preferences. The divergence of mating preferences in correlation with environment is consistent with the classic by-product model of speciation in which premating isolation evolves as a side effect of divergent selection adapting populations to their different environments.

Adaptation, Biological↗
PubMed1991

Species-specific diversity among simian immunodeficiency viruses from African green monkeys.

The prevalence, natural history, and genetic characteristics of simian immunodeficiency virus (SIV) infections in most feral African monkey species are presently unknown, yet this information is essential to elucidate their origin and relationship to other simian and human immunodeficiency viruses. In this study, a combination of classical and molecular approaches were used to identify and characterize SIV isolates from West African green monkeys (Cercopithecus sabaeus) (SIVagm isolates). Four SIVagm viruses from wild-caught West African green monkeys were isolated and analyzed biologically and molecularly. Amplification, cloning, and sequencing of a 279-bp polymerase fragment directly from uncultured peripheral blood mononuclear cells was facilitated by the use of nested polymerase chain reaction. The results indicated that West African green monkeys are naturally infected with SIVs which are closely related to East African SIVagm isolates. However, structural, antigenic, and genetic differences were observed which strongly suggest that the West African green monkey viruses comprise a phylogenetically distinct subgroup of SIVagm. These findings support our previous hypothesis that SIVagm viruses may have evolved and diverged coincident with the evolution and divergence of their African green monkey host. In addition, this study describes a polymerase chain reaction-based approach that allows the identification and molecular analysis of divergent SIV strains directly from primary monkey tissue. This approach, which does not depend on virus isolation methods, should facilitate future studies aimed at elucidating the origins and natural history of SIVs in feral African green monkey populations.

Amino Acid Sequence↗