Partition-free congruence analysis: implications for sensitivity analysis

A criterion is proposed to compare systematic hypotheses based on multiple sources of information under a diverse set of interpretive assumptions (i.e., sensitivity analysis of Wheeler, 1995 ). This metric, the Meta‐Retention Index (MRI), is the retention index (RI) of Farris calculated over the set of conventional homologous qualitative characters (ordered, unordered, Sankoff, etc.) and molecular fragment characters sensu Wheeler (1996, 1999 ). The superiority of this measure to other similar measures (e.g., incongruence length difference test) comes from its independence from partition information. The only values that participate in its calculation are the minimum, maximum and observed cost (= cladogram cost) of each character. The partition (morphology, gene locus) from which the variant may have come is irrelevant. In the special cases where there is only a single data partition, this measure is equivalent to the conventional RI; and in the case where there are single fragment characters per partition (contiguous molecular loci as data sets) the measure is identical to the complement of the Rescaled Incongruence Length Difference (RILD) of Wheeler and Hayashi (1998 ). The MRI can serve as an optimality criterion for deciding among systematic hypotheses based on the same data, but different sets of analysis assumptions (e.g., character weights, indel costs). The MRI may lose discriminatory power in situations where a minority of highly congruent characters is given high weight. This situation can be detected and seems unlikely to occur frequently in real data sets. © The Willi Hennig Society 2006.     

Phylogenetic analysis of Themira (Sepsidae: Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study

In this study we use sensitivity analysis sensu Wheeler (1995 ) for a matrix entirely composed of DNA sequences. We propose that not only congruence but also phylogenetic structure, as measured by character resampling, should be used to choose among competing weighting regimes. An extensive analysis of a five‐gene data set for Themira (Sepsidae: Diptera) reveals that even with different ways of partitioning the data, measures of topological congruence, character incongruence, and phylogenetic structure favor similar weighting regimes involving the down‐weighting of transitions. We furthermore use sensitivity analysis for obtaining empirical evidence that allows us to select weights for third positions, deciding between treating indels as fifth character states or missing values, and choosing between manual and computational alignments. For our data, sensitivity analysis favors manual alignment over a Clustal‐generated numerical alignment, the treatment of indels as fifth character states over considering them missing values, and equal weights for all positions in protein‐encoding genes over the down‐weighting of third positions. Among the topological congruence measures compared, symmetric tree distance performed best. Partitioned Bremer Support analysis reveals that COI contributes the largest amount of support for our phylogenetic tree for Themira. © The Willi Hennig Society 2005.     

Naturally occurring indel variation in the Brassica nigra COL1 gene is associated with variation in flowering time

Previous QTL mapping identified a Brassica nigra homolog to Arabidopsis thaliana CO as a candidate gene affecting flowering time in B. nigra. Transformation of an A. thaliana co mutant with two different alleles of the B. nigra CO (Bni COa) homolog, one from an early-flowering B. nigra plant and one from a late one, did not show any differential effect of the two alleles on flowering time. The DNA sequence of the coding region of the two alleles was also identical, showing that nucleotide variation influencing flowering time must reside outside the coding region of Bni COa. In contrast, the nucleotide sequence of the B. nigra COL1 (Bni COL1) gene located 3.5 kb upstream of Bni COa was highly diverged between the alleles from early and late plants. One indel polymorphism in the Bni COL1 coding region, present in several natural populations of B. nigra, displayed a significant association with flowering time within a majority of these populations. These data indicate that a quantitative trait nucleotide (QTN) affecting flowering time is located within or close to the Bni COL1 gene. The intergenic sequence between Bni COL1 and Bni COa displayed a prominent peak of divergence 1 kb downstream of the Bni COL1 coding region. This region could contain regulatory elements for the downstream Bni COa gene. Our data suggest that a naturally occurring QTN for flowering time affects the function or expression of either Bni COL1 or Bni COa.     

Testing congruence in phylogenomic analysis

Phylogenomic analyses of large sets of genes or proteins have the potential to revolutionize our understanding of the tree of life. However, problems arise because estimated phylogenies from individual loci often differ because of different histories, systematic bias, or stochastic error. We have developed Concaterpillar, a hierarchical clustering method based on likelihood-ratio testing that identifies congruent loci for phylogenomic analysis. Concaterpillar also includes a test for shared relative evolutionary rates between genes indicating whether they should be analyzed separately or by concatenation. In simulation studies, the performance of this method is excellent when a multiple comparison correction is applied. We analyzed a phylogenomic data set of 60 translational protein sequences from the major supergroups of eukaryotes and identified three congruent subsets of proteins. Analysis of the largest set indicates improved congruence relative to the full data set and produced a phylogeny with stronger support for five eukaryote supergroups including the Opisthokonts, the Plantae, the stramenopiles + Apicomplexa (chromalveolates), the Amoebozoa, and the Excavata. In contrast, the phylogeny of the second largest set indicates a close relationship between stramenopiles and red algae, to the exclusion of alveolates, suggesting gene transfer from the red algal secondary symbiont to the ancestral stramenopile host nucleus during the origin of their chloroplast. Investigating phylogenomic data sets for conflicting signals has the potential to both improve phylogenetic accuracy and inform our understanding of genome evolution.     

Natural variation in Arabidopsis lyrata vernalization requirement conferred by a FRIGIDA indel polymorphism

Species share homologous genes to a large extent, but it isnot yet known to what degree the same loci have been targetsfor natural selection in different species. Natural variationin flowering time is determined to a large degree by 2 genes,FLOWERING LOCUS C and FRIGIDA, in Arabidopsis thaliana. Here,we examine whether FRIGIDA has a role in differences in floweringtime between and within natural populations of Arabidopsis lyrata,a close outcrossing perennial relative of A. thaliana. We found2 FRIGIDA sequence variants producing potentially functionalproteins but with a length difference of 14 amino acids. Thesevariants conferred a 15-day difference in flowering time inan association experiment in 2 Scandinavian populations. Thedifference in flowering time between alleles was confirmed withtransformation to A. thaliana. Because the north European late-floweringpopulations harbor both late- and early sequence variants atintermediate frequencies and the late-flowering variant is mostfrequent in the southern early flowering European population,other genetic factors must be responsible for the floweringtime differences between the populations. The length polymorphismoccurs at high frequencies also in several North American populations.The occurrence of functional variants at intermediate frequenciesin several populations suggests that the variation may be maintainedby balancing selection. This is in contrast to A. thaliana,where independent loss-of-function mutations at the FRIGIDAgene are responsible for differences between populations andlocal adaptation.     

A phylogenetic analysis of indel dynamics in the cotton genus

Genome size evolution is a dynamic process involving counterbalancing mechanisms whose actions vary across lineages and over time. Whereas the primary mechanism of expansion, transposable element (TE) amplification, has been widely documented, the evolutionary dynamics of genome contraction have been less thoroughly explored. To evaluate the relative impact and evolutionary stability of the mechanisms that affect genome size, we conducted a phylogenetic analysis of indel rates for 2 genomic regions in 4 Gossypium genomes: the 2 coresident genomes (A(T) and D(T)) of tetraploid cotton and its model diploid progenitors, Gossypium arboreum (A) and Gossypium raimondii (D). We determined the rates of sequence gain or loss along each branch, partitioned by mechanism, and how these changed during species divergence. In general, there has been a propensity toward growth of the diploid genomes and contraction in the polyploid. Most of the size difference between the diploid species occurred prior to polyploid divergence and was largely attributable to TE amplification in the A/A(T) genome. After separating from the true parents of the polyploid genomes, both diploid genomes experienced slower sequence gain than in the ancestor, due to fewer TE insertions in the A genome and a combination of increased deletions and decreased TE insertions in the D genome. Both genomes of the polyploid displayed increased rates of deletion and decreased rates of insertion, leading to a rate of near stasis in D(T) and overall contraction in A(T) resulting in polyploid genome contraction. As expected, TE insertions contributed significantly to the genome size differences; however, intrastrand homologous recombination, although rare, had the most significant impact on the rate of deletion. Small indel data for the diploids suggest the possibility of a bias as the smaller genomes add less or delete more sequence through small indels than do the larger genomes, whereas data for the polyploid suggest increased sequence turnover in general (both as small deletions and small insertions). Illegitimate recombination, although not demonstrated to be a dominant mechanism of genome size change, was biased in the polyploid toward deletions, which may provide a partial explanation of polyploid genomic downsizing.     

GapCoder automates the use of indel characters in phylogenetic analysis

Background

Several ways of incorporating indels into phylogenetic analysis have been suggested. Simple indel coding has two strengths: (1) biological realism and (2) efficiency of analysis. In the method, each indel with different start and/or end positions is considered to be a separate character. The presence/absence of these indel characters is then added to the data set.

Algorithm

We have written a program, GapCoder to automate this procedure. The program can input PIR format aligned datasets, find the indels and add the indel-based characters. The output is a NEXUS format file, which includes a table showing what region each indel characters is based on. If regions are excluded from analysis, this table makes it easy to identify the corresponding indel characters for exclusion.

Discussion

Manual implementation of the simple indel coding method can be very time-consuming, especially in data sets where indels are numerous and/or overlapping. GapCoder automates this method and is therefore particularly useful during procedures where phylogenetic analyses need to be repeated many times, such as when different alignments are being explored or when various taxon or character sets are being explored. GapCoder is currently available for Windows from http://www.home.duq.edu/~youngnd/GapCoder.

     

Demographic costs of Chaoborus-induced defences in Daphnia pulex: a sensitivity analysis

Summary We examined the demographic costs of Chaoborus-induced defensive spine structures in Daphnia pulex. Our aim was to assess the role of resource limitation and the interaction effects of limiting food level and antipredator structures on fitness of D. pulex and to pinpoint those life stages that are most sensitive to changes in the defence regime. Chaoborus-induced and typical morphotypes of D. pulex were reared at high and low food concentrations. Instar-based matrix population models were used to quantify the effects of predator-induction, food and their interaction on fitness of D. pulex. Predator-induction caused a statistically significant reduction in fitness at low food levels, but not at high food levels. Sensitivity analyses revealed that the fitness effects were primarily due to changes in the growth rate in instars 1–5, and secondarily to small reductions in the fertility of instars 5–10. The interaction between Chaoborus exposure and low food concentration was negative, and mediated through growth and fertility components. Both these components were reduced more in the Chaoborus-exposed, low food treatment than would be expected in the absence of interaction.     

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms

We assessed the disease-causing potential of single nucleotide polymorphisms (SNPs) based on a simple set of sequence-based features. We focused on SNPs from the dbSNP database in G-protein-coupled receptors (GPCRs), a large class of important transmembrane (TM) proteins. Apart from the location of the SNP in the protein, we evaluated the predictive power of three major classes of features to differentiate between disease-causing mutations and neutral changes: (i) properties derived from amino-acid scales, such as volume and hydrophobicity; (ii) position-specific phylogenetic features reflecting evolutionary conservation, such as normalized site entropy, residue frequency and SIFT score; and (iii) substitution-matrix scores, such as those derived from the BLOSUM62, GRANTHAM and PHAT matrices. We validated our approach using a control dataset consisting of known disease-causing mutations and neutral variations. Logistic regression analyses indicated that position-specific phylogenetic features that describe the conservation of an amino acid at a specific site are the best discriminators of disease mutations versus neutral variations, and integration of all our features improves discrimination power. Overall, we identify 115 SNPs in GPCRs from dbSNP that are likely to be associated with disease and thus are good candidates for genotyping in association studies.     

Gestation length, mode of delivery, and neonatal line-thickness variation

The transition from an intra- to extra-uterine environment leaves its mark in deciduous teeth (and first permanent molars) as an accentuated enamel incremental ring called the neonatal line (NL). This prominent microfeature separates the enamel formed during intrauterine life from that formed after leaving the womb. However, while the physical structure of this scar is well known, the bases of its formation are still a matter of investigation. In particular, besides the influence of the birth-related abrupt environmental and dietary changes and the role played by physiological factors such as hypocalcaemia, a direct relationship between NL thickness variation and the physical was trauma implied by the birth dynamics, the Caesarean, and the operative modes are apparently associated with the thinnest and the thickest lines, respectively. By using the histological record from a deciduous dental sample (exfoliated crowns) of 100 modern healthy school-aged children (47 males and 53 females) of reported birth histories (normal delivery mode: 55 cases; Caesarean: 40; operative: 5), we investigated the relationships between birth dynamics and NL thickness variation. The Tukey Honest Significant Difference method was used to test the differences between the means of the grouping levels. The results of our histo-morphological investigation do not support the suggestion that Caesarean-born children display, on average, a thinner enamel scar compared to children associated to a normal delivery mode. Rather, our study points to the influence exerted by factors intimately related to gestational length variation on the degree of expression of the line.     

Sequence analysis of phosphoserine-containing peptides. Modification for picomolar sensitivity

Sequencing of phosphoserine-containing peptides yields normally no identifiable PTH-derivatives at those positions where phosphoserine is located. Here a new method is described which allows identification of the position of phosphoserine by chemical modification just before sequence analysis. In a one-step microbatch reaction, phosphoserine present in the intact peptide can be transformed quantitatively into stable derivatives such as beta-methylaminoalanine (MAA), S-ethanolcysteine or S-ethylcysteine. These derivatives are detectable during microsequencing with less than 100 pmol peptide using an Applied Biosystems gas-phase sequencer equipped with an on-line PTH amino acid analyzer.     

Phylocomposer and phylodirector: analysis and visualization of transducer indel models

Finite-state string transducers are probabilistic tools similar to Hidden Markov Models that can be systematically extended to large number of sequences related by indel and substitution processes on phylogenetic trees. The number of states in such models grows exponentially with the number of nodes in the tree, with the consequence that even quite small trees can be difficult to analyze or visualize. Here, we present two tools, phylocomposer and phylodirector, for working with string transducers. The former tool implements previously described composition algorithms for extending transducers to arbitrary tree topologies, while the latter generates short animations for arbitrary input alignments and phylogenetic trees, illustrating the state path through the composed transducer. AVAILABILITY: Phylocomposer and phylodirector are freely available at http://biowiki.org/PhyloComposer and http://biowiki.org/PhyloDirector     

Flood disturbance, algal productivity, and interannual variation in food chain length

The length of a river food chain changed from year to year, shifting with the hydrologic regime. During drought years, grazers suppressed algae across a nutrient gradient, while predators were functionally unimportant. Following flood disturbance, predators suppressed grazers, releasing algae. These results suggest that hydrologic regime, rather than productivity, determines the functional length of this river food chain. Within years, algae and grazer biomass responded to an experimental productivity gradient in patterns predicted by simple trophic models that assume efficient energy transfer. Understanding differences among species within trophic levels, however, was crucial in delineating the controlling interactions.     

Sequence variation of HIV and bioinformatics

The envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) interacts with receptors on the target cell and mediates virus entry by fusing the viral and cell membranes. To maintain the viral infectivity, amino acids that interact with receptors are expected to be more conserved than the other sites on the protein surface. In contrast to the functional constraint of amino acids for the receptor binding, some amino acid changes in this protein may produce antigenic variations that enable the virus to escape from recognition of the host immune system. Therefore, both positive selection (higher fitness) and negative selection (lower fitness) against amino acid changes are taking place during evolution of surface proteins of parasites To elucidate the evolutionary mechanisms of the whole HIV-1 gp120 envelope glycoprotein at the single site level, we collected and analyzed all available sequence data for the protein. By analyzing 186 sequences of the HIV-1 gp120 (subtype B), we reevaluated amino acid variability at the single site level, and estimated the numbers of synonymous and nonsynonymous substitutions at each codon position to detect positive and negative selection. We identified 33 amino acid positions which may be under positive selection. Some of these positions may form discontinuous epitopes. We also analyzed amino acid sequences to find amino acid positions responsible for usage of the second receptor. We found that, in addition to the V3 loop, amino acid variation at residue 440 in C4 region is clearly linked with the usage of CXCR 4.