Evolution of adaptive phenotypic traits without positive Darwinian selection.

Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity-relaxation-mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift. Although the generality of the PRM mechanism is at present unknown, I discuss evidence for its widespread occurrence, including the prevalence of exaptations in evolution, evidence that phenotypic plasticity has preceded adaptation in a number of taxa and evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation, as well as recently reported cases of apparent adaptive evolution over ecological time.

Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef.

Cytotoxic T-lymphocyte (CTL) responses to human immunodeficiency virus arise early after infection, but ultimately fail to prevent progression to AIDS. Human immunodeficiency virus may evade the CTL response by accumulating amino-acid replacements within CTL epitopes. We studied 10 CTL epitopes during the course of simian immunodeficiency virus disease progression in three related macaques. All 10 of these CTL epitopes accumulated amino-acid replacements and showed evidence of positive selection by the time the macaques died. Many of the amino-acid replacements in these epitopes reduced or eliminated major histocompatibility complex class I binding and/or CTL recognition. These findings strongly support the CTL 'escape' hypothesis.

On a limitation of Zeeman polarimetry and imperfect instrumentation in representing solar magnetic fields with weaker polarization signal.

Full disk vector magnetic fields are used widely for developing better understanding of large-scale structure, morphology, and patterns of the solar magnetic field. The data are also important for modeling various solar phenomena. However, observations of vector magnetic fields have one important limitation that may affect the determination of the true magnetic field orientation. This limitation stems from our ability to interpret the differing character of the Zeeman polarization signals which arise from the photospheric line-of-sight vs. the transverse components of the solar vector magnetic field, and is likely exacerbated by unresolved structure (non-unity fill fraction) as well as the disambiguation of the 180° degeneracy in the transverse-field azimuth. Here we provide a description of this phenomenon, and discuss issues, which require additional investigation.

Reduced variance of gene expression at numerous loci in a population of chickens selected for high feather pecking.

Changes in gene expression in response to selection were studied by comparing microarray expression profiles among a population of domestic chickens selected for high feather pecking (FP) with a control population and a population selected for low FP. No transcripts showed significant differences among populations with respect to mean expression scores, but numerous transcripts showed reduced variance in expression scores in the high FP population in comparison to control and low FP populations. The reduction in variance in the high FP population generally involved transcripts whose expression scores had a negatively skewed distribution in the control population but not in the high FP population. A certain number of these transcripts corresponded to genes whose expression was significantly associated with either severe FP (SFP) or gentle FP. The patterns of gene expression associated with SFP and gentle FP were distinct, suggesting that very distinct underlying neural mechanisms underlie these 2 behaviors, with SFP showing more signs of an association with synaptic plasticity and with an immunosuppressive stress response.

Effect of Quantum phytase on nutrient digestibility and bone ash in White Leghorn laying hens fed corn-soybean meal-based diets.

The efficacy of an Escherichia coli 6-phytase supplementation (Quantum) on nutrient digestibility-retention and bone ash in laying hens fed corn-soybean meal (CSM) diets was investigated. White Leghorn hens (Shaver and Bovan strains) were fed CSM diets containing 0.35% (positive control, PC), 0.25% (negative control 1, NC1), or 0.15% (negative control 2, NC2) nonphytate P from 21 to 61 wk of age. Six more diets were manufactured by supplementing the negative control diets with 200, 400, and 600 units per kilogram of exogenous phytase resulting in a total of 9 treatments. Each dietary treatment x strain subclass was replicated twice with 6 hens per replication. Fecal and ileal digesta samples were collected at 42 wk of age to determine apparent nutrient digestibility or retention. Left tibiae were collected at 42 and 61 wk of age to determine bone ash. The coefficients for ileal digestibility and fecal retention for protein were higher (P < 0.05) for the unsupplemented negative control treatments compared with the PC. A linear reduction in phytate digestibility and ileal protein digestibility was reported with increasing levels of phytase to the NC1 diet. Phytase addition to the NC1 treatment resulted in a linear decrease in the digestibility of amino acids except for methionine and proline. Significantly higher phytate digestibility was demonstrated with the NC2 treatment containing 400 units per kilogram of phytase compared with the PC. Tibial bone ash percentage was higher (P < 0.05) in 61-wk-old hens fed 200 or 400 units per kilogram of phytase-supplemented NC2 diets. Significantly higher diet AME and fecal protein retention were demonstrated for Shaver hens in comparison to the Bovan hens. Overall, the Quantum phytase was not efficacious at improving nutrient digestibility-retention in laying hens fed CSM diets deficient in nonphytate P.

The efficacy of quantum phytase in a forty-week production trial using white leghorn laying hens fed corn-soybean meal-based diets.

Microbial phytase is a prominent feed enzyme used in animal feeds, but there is relatively little information on its use in laying hen diets. In this experiment, an Escherichia coli 6-phytase (Quantum) was evaluated for its efficacy in a 40-wk laying hen production trial. A total of 1,080 White Leghorn hens (540 each of Shaver and Bovan strains) were fed mash corn-soybean meal-based diets containing 0.35% (positive control, PC), 0.25% (negative control, NC1), or 0.15% (NC2) nonphytate phosphorus (NPP). Six more diets were manufactured by supplementing the negative control diets with 200, 400, and 600 U/kg of exogenous phytase, resulting in a total of 9 treatments. Each dietary treatment x strain subclass was replicated 4 times with 5 adjoining cages per replicate (3 hens per cage) in a randomized complete block design. Production performance was measured from 21 to 61 wk of age. Only minor differences in production characteristics were found between the PC and NC1 treatments regardless of phytase addition, indicating that 0.25% NPP resulted in P intake that was at or above the hen's requirement. In contrast, the hens fed 0.15% NPP diet without phytase supplementation had significantly (P < 0.05) reduced total hen housed egg production and body weight at 61 wk of age in comparison to the PC treatment, whereas the incidence of soft-shelled, cracked, and broken eggs was increased significantly (P < 0.05) in hens fed the NC2 diet. Addition of phytase to the NC2 diet improved these production characteristics to levels equal or better than the PC diet. The results indicated that Quantum phytase was efficacious in corn-soybean meal-based diets fed to White Leghorn laying hens and can be used to reduce diet supplementation with inorganic phosphorus.

Placental expression and molecular characterization of aromatase cytochrome P450 in the spotted hyena (Crocuta crocuta).

At birth, the external genitalia of female spotted hyenas (Crocuta crocuta) are the most masculinized of any known mammal, but are still sexually differentiated. Placental aromatase cytochrome P450 (P450arom) is an important route of androgen metabolism protecting human female fetuses from virilization in utero. Therefore, placental P450arom expression was examined in spotted hyenas to determine levels during genital differentiation, and to compare molecular characteristics between the hyena and human placental enzymes. Hyena placental P450arom activity was determined at gestational days (GD) 31, 35, 45, 65 and 95 (term, 110), and the relative sensitivity of hyena and human placental enzyme to inhibition by the specific inhibitor, Letrozole, was also examined. Expression of hyena P450arom in placenta was localized by immuno-histochemistry, and a full-length cDNA was cloned for phylogenetic analysis. Aromatase activity increased from GD31 to a peak at 45 and 65, apparently decreasing later in gestation. This activity was more sensitive to inhibition by Letrozole than was human placental aromatase activity. Expression of P450arom was localized to syncytiotrophoblast and giant cells of mid-gestation placentas. The coding sequence of hyena P450arom was 94% and 86% identical to the canine and human enzymes respectively, as reflected by phylogenetic analyses. These data demonstrate for the first time that hyena placental aromatase activity is comparable to that of human placentas when genital differentiation is in progress. This suggests that even in female spotted hyenas clitoral differentiation is likely protected from virilization by placental androgen metabolism. Decreased placental aromatase activity in late gestation may be equally important in allowing androgen to program behaviors at birth. Although hyena P450arom is closely related to the canine enzyme, both placental anatomy and P450arom expression differ. Other hyaenids and carnivores must be investigated to determine the morphological and functional ancestral state of their placentas, as it relates to evolutionary relationships among species in this important taxonomic group.

Natural selection of K13 mutants of Plasmodium falciparum in response to artemisinin combination therapies in Thailand.

Resistance of Plasmodium falciparum to artemisinin combination therapy (ACT) in Southeast Asia can have a devastating impact on chemotherapy and control measures. In this study, the evolution of artemisinin-resistant P. falciparum in Thailand was assessed by exploring mutations in the K13 locus believed to confer drug resistance phenotype. P. falciparum-infected blood samples were obtained from patients in eight provinces of Thailand over two decades (1991-2014; n = 904). Analysis of the K13 gene was performed by either sequencing the complete coding region (n = 259) or mutation-specific PCR-restriction fragment length polymorphism method (n = 645). K13 mutations related to artesunate resistance were detected in isolates from Trat province bordering Cambodia in 1991, about 4 years preceding widespread deployment of ACT in Thailand and increased in frequency over time. Nonsynonymous nucleotide diversity exceeded synonymous nucleotide diversity in the propeller region of the K13 gene, supporting the hypothesis that this diversity was driven by natural selection. No single mutant appeared to be favoured in every population, and propeller-region mutants were rarely observed in linkage with each other in the same haplotype. On the other hand, there was a highly significant association between the occurrence of a propeller mutant and the insertion of two or three asparagines after residue 139 of K13. Whether this insertion plays a compensatory role for deleterious effects of propeller mutants on the function of the K13 protein requires further investigation. However, modification of duration of ACT from 2-day to 3-day regimens in 2008 throughout the country does not halt the increase in frequency of mutants conferring artemisinin resistance phenotype.

Circumsporozoite protein genes of malaria parasites (Plasmodium spp.): evidence for positive selection on immunogenic regions.

The circumsporozoite (CS) protein is a cell surface protein of the sporozoite, the stage of the life cycle of malaria parasites (Plasmodium spp.) that infects the vertebrate host. Analysis of DNA sequences supports the hypothesis that in Plasmodium falciparum, positive Darwinian selection favors diversity in the T-cell epitopes (peptides presented to T cells by host MHC molecules) of the CS protein. In gene regions encoding T cell epitopes of P. falciparum, the rate of nonsynonymous nucleotide substitution is significantly higher than that of synonymous substitution, whereas this is not true of other gene regions. Furthermore nonsynonymous nucleotide substitutions in these regions cause a change of amino acid residue charge significantly more frequently than expected by chance. By contrast, in Plasmodium cynomolgi, the same regions show no evidence of positive selection, and residue charge is conserved. The CS protein has a central repeat region, which is the target of host antibodies. In P. falciparum, the amino acid sequence of the repeat region is conserved within and between alleles. In P. cynomolgi, on the other hand, there is evidence that positive selection has favored evolution of two different repeat types within a given allele.

Ancient interlocus exon exchange in the history of the HLA-A locus.

The major histocompatibility complex (MHC) in humans and chimpanzees includes three classical class I loci, A, B and C, which encode glycoproteins expressed on the surface of all nucleated cells. There are also several nonclassical class I loci including E, which have more limited expression. By analyzing published sequences, we have shown that in exons 4 and 5, A locus alleles from both humans and chimpanzees are much more similar to E than to B or C alleles, whereas in exons 2 and 3 alleles from all three classical class I loci are much more similar to each other than any one is to E. We propose that some 20 million years ago, interlocus recombination led to the formation of a hybrid gene in which exons 2 and 3 were derived from the original A locus and exons 4 and 5 were derived from the E locus. The fact that such an ancient event can still be detected suggests that interlocus recombination is rare in the MHC and does not significantly contribute to MHC polymorphism, which is known to be extremely high. The present finding, however, supports Gilbert's idea that exons in a gene may occasionally be replaced by those from another gene in the evolutionary process.

Contrasting roles of interallelic recombination at the HLA-A and HLA-B loci.

A statistical study of DNA sequences of alleles at the highly polymorphic class I MHC loci of humans, HLA-A and HLA-B, showed evidence of both large-scale recombination events (involving recombination of exons 1-2 of one allele with exons 3-8 of another) and small-scale recombination events (involving apparent exchange of short DNA segments). The latter events occurred disproportionately in the region of the gene encoding the antigen recognition site (ARS) of the class I molecule. Furthermore, they involved the ARS codons which are under the strongest selection favoring allelic diversity at the amino acid level. Thus, the frequency of recombinant alleles appears to have been increased by some form of balancing selection (such as overdominant selection) favoring heterozygosity in the ARS. These analyses also revealed a striking difference between the A and B loci. Recombination events appear to have occurred about twice as frequently at the B locus, and recombinants at the B locus were significantly more likely to affect polymorphic sites in the ARS. At the A locus, there are well-defined allelic lineages that have persisted since prior to the human-chimpanzee divergence; but at the B locus, there is no evidence for such long-lasting allelic lineages. Thus, relatively frequent interallelic recombination has apparently been a feature of the long-term evolution of the B locus but not of the A locus.

Independent origin of IFN-alpha and IFN-beta in birds and mammals.

Phylogenetic analysis of type I interferon (IFN) from birds and mammals strongly supported the hypothesis that the gene duplication giving rise to the alpha and beta families of mammalian IFN occurred after the divergence of birds from mammals, whereas the bird IFN that have been designated alpha and beta duplicated independently in the avian lineage. Therefore, IFN designated alpha and beta in birds are not orthologous to those similarly designated in mammals.

Natural selection and the evolutionary history of major histocompatibility complex loci.

The major histocompatibility complex (MHC) is a multi-gene family unique to the vertebrates, whose products function to present peptides to T cells. Certain MHC loci are highly polymorphic, and this polymorphism is maintained by a form of balancing selection, probably overdominant selection. This selection has several consequences for MHC biology that make these genes different from neutrally evolving genes: an enhanced rate of nonsynonymous nucleotide substitution in codons encoding the peptide-binding region; long-lasting ("trans-species") polymorphism; and homogenization of introns relative to exons as a result of recombination and subsequent genetic drift. The MHC also reveals evidence of processes shared with other multi-gene families, including gene duplication and deletion and a low level of inter-locus recombination.

Rates of amino acid evolution in the 26- and 28-kDa glutathione S-transferases of Schistosoma.

Statistical analysis of glutathione S-transferase (GST) sequences of Schistosoma mansoni, Schistosoma japonicum, and other animals revealed that, in comparison both to the related mammalian alpha GSTs and to Schistosoma 26-kDa GSTs, the 28-kDa GSTs of Schistosoma have evolved unusually rapidly at the amino acid level in the ordinarily conserved N-terminal portion of the molecule. Because this rapid rate of evolution is reflected at the amino acid level and at nonsynonymous nucleotide sites but not at synonymous nucleotide sites, it must be due to a relaxation of functional constraint on the N-terminal region of the Schistosoma 28-kDa GSTs rather than to a high mutation rate. By contrast, the 26-kDa GSTs of Schistosoma not only show a slower rate of amino acid evolution in the N-terminal portion than the 28-kDa GSTs but also have evolved more slowly in the C-terminal portion than have the related mammalian mu GSTs. The two 26-kDa GSTs of S. mansoni show particularly strong amino acid conservation between one another in the N-terminal region and a predominance of conservative amino acid replacements.

Natural selection on Plasmodium surface proteins.

Numbers of synonymous (ds) and nonsynonymous (dN) nucleotide substitutions per site were analysed in eight polymorphic Plasmodium genes: circumsporozoite protein gene (CSP), sporozoite surface protein 2 (thrombospondin related anonymous protein, TRAP), merozoite surface antigen 2 (MSA-2), apical membrane antigen 1 (PF83), liver-stage antigen-1 (LSA-1), knob-associated histidine-rich protein (KAHRP), ring-infected erythrocyte surface antigen (RESA) and S-antigen. In certain regions of genes coding for proteins of the sporozoite and merozoite surface (CSP, TRAP, MSA-2 and PF83), dN was significantly greater than dS. This unusual pattern of nucleotide substitution is indicative of positive Darwinian selection acting to promote diversity at the amino-acid level; thus our results suggest that the sporozoite and merozoite surface proteins are under positive selection, presumably exerted by the host immune system. No such pattern of substitution was observed on LSA-1, KAHRP, RESA, or S-antigen. Observed patterns of nucleotide substitution were not explicable by nucleotide content bias. G + C content in the 5' nonrepeat region of CSP in nine Plasmodium species was positively correlated with that in the 3' nonrepeat region; however, there was no relationship between G + C content and the ratio dS/dN in either CSP or a larger sample of all regions of all genes analysed.

The evolution of functionally novel proteins after gene duplication.

A widely cited model of the evolution of functionally novel proteins (here called the model of mutation during non-functionality (MDN model)) holds that, after gene duplication, one gene copy is redundant and free to accumulate substitutions at random. By chance, some of these substitutions may suit the protein encoded by such a non-functional gene to a new function, which it can subsequently assume. Several lines of evidence contradict this hypothesis: (i) comparison of expressed duplicate genes from the tetraploid frog Xenopus laevis suggests that such genes are subject to purifying selection and are thus not free to accumulate substitutions at random; (ii) in a number of multi-gene families, there is now evidence that functionally distinct proteins have arisen not as a result of chance fixation of neutral variants but rather as a result of positive Darwinian selection; and (iii) the phenomenon of gene sharing, in which a single gene encodes a protein having two distinct functions, shows that gene duplication is not a necessary prerequisite to the evolution of a new protein function. A model for the evolution of new protein is proposed under which a period of gene sharing ordinarily precedes the evolution of functionally distinct proteins. Gene duplication then allows each daughter gene to specialize for one of the functions of the ancestral gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum.

It has been proposed that the virulent human malaria parasite Plasmodium falciparum underwent a recent severe population bottleneck. In order to test this hypothesis, we estimated the effective population size of this species from the patterns of nucleotide substitution at 23 nuclear protein-coding loci, using a variety of methods based on coalescent theory. Both simple methods and phylogenetically based maximum-likelihood methods yielded the conclusion that the effective population size of this species has been of the order of at least 10(5) for the past 300,000-400,000 years.

Evolutionary change of predicted cytotoxic T cell epitopes of dengue virus.

Peptides bound by human class I major histocompatibility complex molecules and presented to cytotoxic T cells (CTL) were predicted by a computer algorithm, and changes in these predicted CTL epitopes (pCTLE) were reconstructed by maximum parsimony in a phylogeny of complete genotypes of dengue virus, West Nile virus (WNV), and Japanese encephalitis virus (JEV). In a clade including dengue virus serotypes 1 and 3 (D1V and D3V), pCTLE were lost over evolutionary time at a greater rate than new ones were gained. A similar but less pronounced trend was seen in the other dengue serotypes but not in WNV and JEV. The loss of pCTLE predicted to be restricted by HLA-B(*)2705 was particularly pronounced in D1V and D3V. Since dengue is endemic in humans, while WNV and JEV are not, these results are consistent with CTL-driven selection on dengue viruses, particularly, D1V and D3V.

Allelic variation in the circumsporozoite protein of Plasmodium falciparum from Thai field isolates.

Allelic variation in the Plasmodium falciparum circumsporozoite (CS) protein gene has been examined by sequencing the entire gene in 15 isolates from an endemic area of Thailand. The isolates contain a total of six new allelic forms of the tetrapeptide repeats and eight variants of the T cell epitope (TCE) region of the CS gene. All nucleotide substitutions in the TCE are nonsynonymous. There is no apparent association between the sequence patterns in the repeats and in the TCE. Comparison of the TCE with published sequences has shown that most variants of our isolates are not identical to those found in different geographic areas, suggesting geographic variation in genetic diversity of the CS protein. In a phylogenetic tree, the new Thai alleles did not cluster together, suggesting a considerable heterogeneity within some geographic areas. Furthermore, analyses of tetrapeptide repeats from a number of isolates and strains showed evidence of three genetic mechanisms for the generation of variation in the repeats of the CS gene: point mutation, duplication of one or more repeat units, and intragenic recombination.

Genomic catastrophism and the origin of vertebrate immunity.

Genomic catastrophism is the belief that unique genetic events, unlike those observed in recent evolutionary history, played a key role in the origin of vertebrate adaptations. Catastrophist hypotheses have been particularly popular is accounting for the origin of vertebrate specific immunity. Two major such hypotheses involve genome duplication by polyploidization and horizontal gene transfer. Recent analyses lead to decisive rejection of the widely cited hypothesis that the vertebrate genome underwent two rounds of genome duplication, and theoretical considerations suggest that genome duplication is unlikely to lead to new adaptive advances. Likewise, the evidence that key elements of the vertebrate immune system arose by horizontal transfer from a bacterium or by incorporation of a transposable element into the vertebrate genome remains relatively weak. Thus, at present, a uniformitarian view of the origin of the vertebrate immune system seems more reasonable, especially given the longer time-frame for vertebrate evolution indicated by molecular data.