Estimation of evolutionary distances between nucleotide sequences

A formal mathematical analysis of the substitution process in nucleotide sequence evolution was done in terms of the Markov process. By using matrix algebra theory, the theoretical foundation of Barry and Hartigan's (Stat. Sci. 2:191–210, 1987) and Lanave et al.'s (J. Mol. Evol. 20:86–93, 1984) methods was provided. Extensive computer simulation was used to compare the accuracy and effectiveness of various methods for estimating the evolutionary distance between two nucleotide sequences. It was shown that the multiparameter methods of Lanave et al.'s (J. Mol. Evol. 20:86–93, 1984), Gojobori et al.'s (J. Mol. Evol. 18:414–422, 1982), and Barry and Hartigan's (Stat. Sci. 2:191–210, 1987) are preferable to others for the purpose of phylogenetic analysis when the sequences are long. However, when sequences are short and the evolutionary distance is large, Tajima and Nei's (Mol. Biol. Evol. 1:269–285, 1984) method is superior to others.     

The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments

How to sample alignments from their posterior probability distribution given two strings is shown. This is extended to sampling alignments of more than two strings. The result is first applied to the estimation of the edges of a given evolutionary tree over several strings. Second, when used in conjunction with simulated annealing, it gives a stochastic search method for an optimal multiple alignment.Correspondence to: L. Allison     

Analysis of peptides from known proteins: Clusterization in sequence space

A combinatorial sequence space (CSS) model was introduced to represent sequences as a set of overlapping k-tuples of some fixed length which correspond to points in the CSS. The aim was to analyze clusterization of protein sequences in the CSS and to test various hypotheses about the possible evolutionary basis of this clusterization. The authors developed an easy-to-use technique which can reveal and analyze such a clusterization in a multidimensional CSS. Application of the technique led to an unexpectedly high clusterization of points in the CSS corresponding to k-tuples from known proteins. The clusterization could not be inferred from nonuniform amino acid frequencies or be explained by the influence of homologous data. None of the tested possible evolutionary and structural factors could explain the clusterization observed either. It looked as if certain protein sequence variations occurred and were fixed in the early course of evolution. Subsequent evolution (predominantly neutral) allowed only a limited number of changes and permitted new variants which led to preservation of certain k-tuples during the course of evolution. This was consistent with the theory of exon shuffling and protein block structure evolution. Possible applications of sequence space features found were also discussed.Correspondence to: H.A. Lim     

Inefficient nitrogen resorption in genets of the actinorhizal nitrogen fixing shrubComptonia peregrina: physiological ineptitude or evolutionary tradeoff?

Nutrient resorption was measured in an actinorhizal nitrogen-fixing shrub,Comptonia peregrina, for five years in the understory of a deciduous oak forest in Rhode Island, USA. Mean resorption of nitrogen was extremely inefficient (11%) compared to most deciduous species (50%+), yet resorption of phosphorus was efficient (53%) and comparable to other species. Of the seven additional nutrients studied, only copper (6%) and zinc (10%) were resorbed from senescing leaves. Resorption of nitrogen (5%–20%) and phosphorus (40%–71%) varied significantly among years. Copper was resorbed from leaves in three years and accreted into leaves in two years. Five-year resorption means differed among individual genets by as much as a factor of 2.5 for nitrogen, and 1.3 for phosphorus. Resorption of nitrogen, copper, and zinc were highly correlated, yet resorption of phosphorus remained autonomous from other nutrients. The ecophysiological tradeoffs inComptonia which have resulted in the cooccurence of actinorhizal nitrogen fixation, inefficient nitrogen resorption, and efficient phosphorus resorption suggest that plant nutrient status does have an impact on resorption efficiency and that the evolution of nutrient conservation strategies is nutrient-specific.     

Game theory-based stakeholder analysis of marine nature reserves and its case studies in Guangdong Province,China

Marine nature reserves (MNRs) play an important role in biodiversity conservation and ecosystem restoration, which are valuable for marine resource protection in China. Many stakeholders are involved in MNRs. The interactions between MNR managers and other stakeholders affect the effectiveness of MNR management. This work divided MNR stakeholders into three categories and applied the analytical hierarchy process (AHP) to identify the key stakeholders. The game model was set up to analyze the strategies of MNR staff and stakeholders. The situation of key stakeholders and management was studied in two MNRs in Guangdong Province through field research and questionnaires. The results showed that fishermen were the main stakeholders in the two cases. The strategies adopted by MNR staff to improve the efficiency of law enforcement and decrease the probability of illegal activities of fishermen are to increase penalties, improve the arrest rate of illegal activities, and reduce the cost of law enforcement per patrol. We suggested that the fishermen’s negative impacts could be minimized by establishing a market management system to reduce illegal earnings, a record-keeping system to share additional benefits only with the fishermen who comply with the law, and an association mechanism in the coastal province to control illegal fishing across provincial boundaries. Identifying key stakeholders and analyzing their relationships could be helpful to find out the best strategy for different MNRs. Building a community of shared interests among various stakeholders could be a promising way to resolve conflicts and improve management effectiveness in MNRs.     

Identifying plant functional types using floristic data bases: Ecological correlates of plant range size

Abstract. In an effort to identify ‘plant functional types’, the islands floras of Great Britain and Kríti (Crete, Greece) were examined separately for ecological correlates of plant range size. Plant functional types (PFTs) were defined here as categories into which plants could be grouped on the basis of attributes that predict greater or lesser sensitivity to ecological variability. Plant range size indicates commonness of a species and was assumed to be a proxy for ‘ecological flexibility’, i.e. species of larger range sizes can better withstand environmental change and differences than species of smaller range sizes. Using evolutionary comparative methods that account for the effect of taxonomic relatedness, both floras were investigated for the effects on range size of woodiness vs. non-woodiness, trees vs. shrubs, trees vs. herbs and shrubs vs. herbs. The British flora was examined additionally for the effects of wind- vs. non-wind-pollination, self vs. animal pollination and animal vs. non-animal fruit dispersal on range size. Two analyses showed significant effects on range size: for British species, trees had larger ranges than shrubs, and wind- pollinated species had larger ranges than non-wind-pollinated species. It is suggested that the lack of a similar pattern for shrubs and trees in Kríti is because the lower water availability of Kríti imbues shrubs with an ecophysiological advantage not relevant in plants of Great Britain. That trees have larger range sizes than shrubs in Great Britain is ascribed to the greater importance of competition for light when other factors are not at issue. The greater range of wind-pollinated than non-windpollinated species in Great Britain is postulated to be because both mutualists must be capable of invading new areas. This may be termed a ‘cost of mutualism’. In terms of PFTs, the results indicate that ‘life-form’ is too broad a classification category by which to differentiate relative sensitivity to environmental variability in Great Britain, in that there were significant differences in range size of trees and shrubs, but not between either of the two categories and herbs, or between woody and non-woody plants. Although pollination type may predict relative sensitivity to variation in Great Britain, dispersal type will not. Finally, differences between Great Britain and Kríti in relative range size patterns suggests that plant functional types may be specific to a region or set of conditions.     

Mitochondrial DNA sequences of various species of the genus Equus with special reference to the phylogenetic relationship between Przewalskii's wild horse and domestic horse

The noncoding region between tRNA^Pro and the large conserved sequence block is the most variable region in the mammalian mitochondrial DNA D-loop region. This variable region (ca. 270 bp) of four species of Equus, including Mongolian and Japanese native domestic horses as well as Przewalskii's (or Mongolian) wild horse, were sequenced. These data were compared with our recently published Thoroughbred horse mitochondrial DNA sequences. The evolutionary rate of this region among the four species of Equus was estimated to be 2–4 × 10^–8 per site per year. Phylogenetic trees of Equus species demonstrate that Przewalskii's wild horse is within the genetic variation among the domestic horse. This suggests that the chromosome number change (probably increase) of the Przewalskii's wild horse occurred rather recently.Correspondence to: N. Ishida     

Domain Evolution in the α-Amylase Family

The available amino acid sequences of the α-amylase family (glycosyl hydrolase family 13) were searched to identify their domain B, a distinct domain that protrudes from the regular catalytic (β/α)₈-barrel between the strand β3 and the helix α3. The isolated domain B sequences were inspected visually and also analyzed by Hydrophobic Cluster Analysis (HCA) to find common features. Sequence analyses and inspection of the few available three-dimensional structures suggest that the secondary structure of domain B varies with the enzyme specificity. Domain B in these different forms, however, may still have evolved from a common ancestor. The largest number of different specificities was found in the group with structural similarity to domain B from Bacillus cereus oligo-1,6-glucosidase that contains an α-helix succeeded by a three-stranded antiparallel β-sheet. These enzymes are α-glucosidase, cyclomaltodextrinase, dextran glucosidase, trehalose-6-phosphate hydrolase, neopullulanase, and a few α-amylases. Domain B of this type was observed also in some mammalian proteins involved in the transport of amino acids. These proteins show remarkable similarity with (β/α)₈-barrel elements throughout the entire sequence of enzymes from the oligo-1,6-glucosidase group. The transport proteins, in turn, resemble the animal 4F2 heavy-chain cell surface antigens, for which the sequences either lack domain B or contain only parts thereof. The similarities are compiled to indicate a possible route of domain evolution in the α-amylase family. Received: 4 December 1996 / Accepted: 13 March 1997