A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes

We recently developed a method for producing comprehensive gene and species phylogenies from unaligned whole genome data using singular value decomposition (SVD) to analyze character string frequencies. This work provides an integrated gene and species phylogeny for 64 vertebrate mitochondrial genomes composed of 832 total proteins. In addition, to provide a theoretical basis for the method, we present a graphical interpretation of both the original frequency matrix and the SVD-derived matrix. These large matrices describe high-dimensional Euclidean spaces within which biomolecular sequences can be uniquely represented as vectors. In particular, the SVD-derived vector space describes each protein relative to a restricted set of newly defined, independent axes, each of which represents a novel form of conserved motif, termed a correlated peptide motif. A quantitative comparison of the relative orientations of protein vectors in this space provides accurate and straightforward estimates of sequence similarity, which can in turn be used to produce comprehensive gene trees. Alternatively, the vector representations of genes from individual species can be summed, allowing species trees to be produced.     

The fast-slow continuum in mammalian life history: an empirical reevaluation

Many life-history traits co-vary across species, even when body size differences are controlled for. This phenomenon has led to the concept of a "fast-slow continuum," which has been influential in both empirical and theoretical studies of life-history evolution. We present a comparative analysis of mammalian life histories showing that, for mammals at least, there is not a single fast-slow continuum. Rather, both across and within mammalian clades, the speed of life varies along at least two largely independent axes when body size effects are removed. One axis reflects how species balance offspring size against offspring number, while the other describes the timing of reproductive bouts.     

Functional substitution of an essential yeast RNA polymerase subunit by a highly conserved mammalian counterpart.

We isolated the cDNA encoding the homolog of the Saccharomyces cerevisiae nuclear RNA polymerase common subunit RPB6 from hamster CHO cells. Alignment of yeast RPB6 with its mammalian counterpart revealed that the subunits have nearly identical carboxy-terminal halves and a short acidic region at the amino terminus. Remarkably, the length and amino acid sequence of the hamster RPB6 are identical to those of the human RPB6 subunit. The conservation in sequence from lower to higher eukaryotes also reflects conservation of function in vivo, since hamster RPB6 supports normal wild-type yeast cell growth in the absence of the essential gene encoding RPB6.     

The root of the mammalian tree inferred from whole mitochondrial genomes

Morphological and molecular data are currently contradictory over the position of monotremes with respect to marsupial and placental mammals. As part of a re-evaluation of both forms of data we examine complete mitochondrial genomes in more detail. There is a particularly large discrepancy in the frequencies of thymine and cytosine (T-C) between mitochondrial genomes that appears to affect some deep divergences in the mammalian tree. We report that recoding nucleotides to RY-characters, and partitioning maximum-likelihood analyses among subsets of data reduces such biases, and improves the fit of models to the data, respectively. RY-coding also increases the signal on the internal branches relative to external, and thus increases the phylogenetic signal. In contrast to previous analyses of mitochondrial data, our analyses favor Theria (marsupials plus placentals) over Marsupionta (monotremes plus marsupials). However, a short therian stem lineage is inferred, which is at variance with the traditionally deep placement of monotremes on morphological data.     

The preference of the mitochondrial endonuclease for a conserved sequence block in mitochondrial DNA is highly conserved during mammalian evolution.

Endonuclease activity identified in crude preparations of rat and human heart mitochondria has each been partially purified and characterized. Both the rat and human activities purify as a single enzyme that closely resembles the endonuclease of bovine-heart mitochondria (Cummings, O.W. et. al. (1987) J. Biol. Chem. 262:2005-2015). All three enzymes, for example elute similarly during gel filtration and DNA-cellulose chromatography, and exhibit similar enzymatic properties. Although the nucleotide sequences of the mtDNAs indicate that there has occurred an unusual degree of divergence in the displacement-loop region during mammalian evolution, the nucleotide specificities of the mt endonucleases appear highly conserved and show a striking preference for an evolutionarily-conserved sequence tract that is located upstream from the heavy (H)-strand origin of DNA replication (OriH).     

Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology,branch lengths,and bootstrap support

We have investigated the effects of different among-site rate variation models on the estimation of substitution model parameters, branch lengths, topology, and bootstrap proportions under minimum evolution (ME) and maximum likelihood (ML). Specifically, we examined equal rates, invariable sites, gamma-distributed rates, and site-specific rates (SSR) models, using mitochondrial DNA sequence data from three protein-coding genes and one tRNA gene from species of the New Zealand cicada genus Maoricicada. Estimates of topology were relatively insensitive to the substitution model used; however, estimates of bootstrap support, branch lengths, and R-matrices (underlying relative substitution rate matrix) were strongly influenced by the assumptions of the substitution model. We identified one situation where ME and ML tree building became inaccurate when implemented with an inappropriate among-site rate variation model. Despite the fact the SSR models often have a better fit to the data than do invariable sites and gamma rates models, SSR models have some serious weaknesses. First, SSR rate parameters are not comparable across data sets, unlike the proportion of invariable sites or the alpha shape parameter of the gamma distribution. Second, the extreme among-site rate variation within codon positions is problematic for SSR models, which explicitly assume rate homogeneity within each rate class. Third, the SSR models appear to give severe underestimates of R-matrices and branch lengths relative to invariable sites and gamma rates models in this example. We recommend performing phylogenetic analyses under a range of substitution models to test the effects of model assumptions not only on estimates of topology but also on estimates of branch length and nodal support.     

The zygomaticotemporal branch of the trigeminal nerve: an anatomical study

This study was conducted to determine the site of emergence of the zygomaticotemporal branch of the trigeminal nerve from the temporalis muscle and to identify the number of its accessory branches and their locations. A pilot study, conducted on the same number of patients, concluded that the main zygomaticotemporal branch emerges from the deep temporal fascia at a point on average 17 mm lateral and 6 mm cephalad to the lateral palpebral commissure, commonly referred to as the lateral canthus. These measurements, however, were obtained after dissection of the temporal area, rendering the findings less reliable. The current study included 20 consecutive patients, 19 women and one man, between the ages of 26 and 85 years, with an average age of 47.6 years. Those who had a history of previous trauma or surgery in the temple area were excluded. Before the start of the endoscopic forehead procedure, the likely topographic site of the zygomaticotemporal branch was marked 17 mm lateral and 6 mm cephalad to the lateral orbital commissure on the basis of the information extrapolated from the pilot study. The surface mark was then transferred to the deeper layers using a 25-gauge needle stained with brilliant green. After endoscopic exposure of the marked site, the distance between the main branch of the trigeminal nerve or its accessory branches and the tattoo mark was measured in posterolateral and cephalocaudal directions. In addition, the number and locations of the accessory branches of the trigeminal nerve were recorded. On the left side, the average distance of the emergence site of the main zygomaticotemporal branch of the trigeminal nerve from the palpebral fissure was 16.8 mm (range, 12 to 31 mm) in the posterolateral direction and an average of 6.4 mm (range, 4 to 11 mm) in the cephalad direction. On the right side, the average measurements for the main branch were 17.1 mm (range, 15 to 21 mm) in the lateral direction and 6.65 mm (range, 5 to 11 mm) in the cephalic direction. Three types of accessory branches were found in relation to the main branch: (1) accessory branch cephalad, (2) accessory branch lateral, and (3) accessory branches in the immediate vicinity of the main branch. This anatomical information has proven colossally helpful in injection of botulinum toxin A in the temporalis muscle to eliminate the trigger sites in the parietotemporal region and surgical management of migraine headaches triggered from this zone.     

The fast–slow continuum and mammalian life-history patterns: an empirical evaluation

The fast–slow continuum hypothesis has been proposed to explain the diversity of life-history patterns exhibited by biological populations, but the quantification and population-dynamic consequences of the continuum has remained unclear. I used the ratio of fertility rate to age at first reproduction (F/α ratio) to quantify the tempo of life-history of 138 populations of mammals, and investigated the life-history and population-dynamic consequences of being “fast” or “slow”. “Fast” mammals (F/α>0.60) were characterized by early maturity, short lifespans, low survival rates, and high fertility and projected population growth rate (λ) compared to “slow” (F/α<0.15) mammals. In “fast” populations, λ was overwhelmingly most sensitive to changes in reproductive parameters (age at first reproduction and fertility rates) and relatively insensitive to changes in survival rates. In “slow” populations, λ was very sensitive to changes in juvenile or adult survival rates, and relatively insensitive to changes in reproductive parameters. The pattern of relationships between the F/α ratio and life-history variables, λ, and elasticity of λ to changes in life-history variables persisted even after the effects of body size and phylogeny were statistically removed. These results suggest that fast–slow continuum in mammalian life-history is independent of body size or phylogeny, that the F/α ratio adequately quantifies the position of a population along a fast–slow continuum, and that the tempo of life- histories has substantial population-dynamic consequences.

Zusammenfassung

Die r-K-Kontinuum-Hypothese wurde aufgestellt, um die Diversität von ,,life-history“-Mustern biologischer Populationen zu erklären, aber die Quantifizierung und die Kosnsequenzen für die Populationsdynamik des Kontinuums blieben unklar. Ich benutze das verhältnis der Fortpflanzungsrate zum Fortpflanzungsalter (F/α-Verhältnis) um die Geschwindigkeit der ,,life-history“ von 138 Populationen von Säugetieren zu quantifizieren und untersuchte die Konsequenzen fur die Lebensweise sowie die Populationsdynamik des,,schnell“oder,,langsam “-Seins. ,,Schnelle“Säugetiere (F/α>0.60) waren durch eine frühe Reife, kurze Lebenszeiten, geringe Überlebensraten sowie durch eine große Fertilität und hochgerechnete Populationswachstumsrate (λ) im Vergleich zu ,,langsamen“(F/α<0.15) Säugetieren charakterisiert. In ,,schnellen“ Population reagierte (λ) überwältigend sensibel auf Änderungen in den Fortpflanzungsparametern (Fortpflanzunsalter und Fertilitätsrate) und relativ gering auf Veräanderungen in der Überlebensrate. In ,,langsamen“ Populationen reagierte (λ) sehr sensibel auf Veräanderungen in den reproduktiven Parametern. Das Muster der Beziehung zwischen dem (F/α-Verhältnis) und den Variablen der ,,life-history“,λ, und die Elastizität von λ gegenüber Veränderungen in den variablen der Lebensweise bliev sogar bestehen, nachdem die Effekte von Körpergröße und Phylogenese statistisch eliminiert wurden. Diese Ergebnisse lassen vermuten, dass das r-K-Kontinuum in der ,,life-history“der Säugetiere unabhängig von der Körpergröße und Phylogenie ist, dass das F/α-Verhältnis die Position einer Population im r-K-Kontinuum quantifiziert und dass die Geschwindigkeit der,,life-history“beachtliche konsequenzen fur die Populationsdynamik hat.     

The effect of family structure on the likelihood for kin-biased distribution: an empirical study of brown trout populations

This study is aimed at evaluating the likelihood that kin-biased distribution will be expressed or detected in a range of brown trout ( Salmo trutta ) populations as a function of family size. Microsatellite analysis indicated that fewer full- and half-siblings were found in populations with larger effective population sizes, while more full- and half-siblings were found in populations with lower effective population size. It is suggested that kin-biased distribution and hence kin-biased behaviours are not likely to be expressed equally frequently in all populations since the number of close relatives will vary among populations and, hence, the opportunity for relatives to interact differs among populations. These findings can, at least partly, explain the discrepancy among previous studies of kin-biased distribution in wild salmonids under natural conditions. Effective population size could, hence, be used to predict the salmonid populations in which kin-biased distribution are more likely to occur and be detected.     

The devil in the details: interactions between the branch-length prior and likelihood model affect node support and branch lengths in the phylogeny of the Psoraceae

In popular use of Bayesian phylogenetics, a default branch-length prior is almost universally applied without knowing how a different prior would have affected the outcome. We performed Bayesian and maximum likelihood (ML) inference of phylogeny based on empirical nucleotide sequence data from a family of lichenized ascomycetes, the Psoraceae, the morphological delimitation of which has been controversial. We specifically assessed the influence of the combination of Bayesian branch-length prior and likelihood model on the properties of the Markov chain Monte Carlo tree sample, including node support, branch lengths, and taxon stability. Data included two regions of the mitochondrial ribosomal RNA gene, the internal transcribed spacer region of the nuclear ribosomal RNA gene, and the protein-coding largest subunit of RNA polymerase II. Data partitioning was performed using Bayes' factors, whereas the best-fitting model of each partition was selected using the Bayesian information criterion (BIC). Given the data and model, short Bayesian branch-length priors generate higher numbers of strongly supported nodes as well as short and topologically similar trees sampled from parts of tree space that are largely unexplored by the ML bootstrap. Long branch-length priors generate fewer strongly supported nodes and longer and more dissimilar trees that are sampled mostly from inside the range of tree space sampled by the ML bootstrap. Priors near the ML distribution of branch lengths generate the best marginal likelihood and the highest frequency of "rogue" (unstable) taxa. The branch-length prior was shown to interact with the likelihood model. Trees inferred under complex partitioned models are more affected by the stretching effect of the branch-length prior. Fewer nodes are strongly supported under a complex model given the same branch-length prior. Irrespective of model, internal branches make up a larger proportion of total tree length under the shortest branch-length priors compared with longer priors. Relative effects on branch lengths caused by the branch-length prior can be problematic to downstream phylogenetic comparative methods making use of the branch lengths. Furthermore, given the same branch-length prior, trees are on average more dissimilar under a simple unpartitioned model compared with a more complex partitioned models. The distribution of ML branch lengths was shown to better fit a gamma or Pareto distribution than an exponential one. Model adequacy tests indicate that the best-fitting model selected by the BIC is insufficient for describing data patterns in 5 of 8 partitions. More general substitution models are required to explain the data in three of these partitions, one of which also requires nonstationarity. The two mitochondrial ribosomal RNA gene partitions need heterotachous models. We found no significant correlations between, on the one hand, the amount of ambiguous data or the smallest branch-length distance to another taxon and, on the other hand, the topological stability of individual taxa. Integrating over several exponentially distributed means under the best-fitting model, node support for the family Psoraceae, including Psora, Protoblastenia, and the Micarea sylvicola group, is approximately 0.96. Support for the genus Psora is distinctly lower, but we found no evidence to contradict the current classification.     

The shape of mammalian phylogeny: patterns, processes and scales

Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'-points at which net diversification rate has changed-identifying 15 significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of 'rules'. Third, we simulate six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions of geographical or niche space.     

The impact of heterogeneous multi-core clusters on graph partitioning: an empirical study

The advent of multi-core architectures provides an opportunity for accelerating parallelism in mesh-based applications. This multi-core environment, however, imposes challenges not addressed by conventional graph-partitioning techniques that are originally designed for distributed-memory uniprocessors. As the first step to exploit the multi-core platform, this paper presents experimental evaluation to understand partitioning performance on small-scaled heterogeneous multi-core clusters. With results and analyses gathered, we propose a hierarchical framework for resource-aware graph partitioning on heterogeneous multi-core clusters. Preliminary evaluation demonstrates the potential of the framework and motivates directions for incorporating application requirements into graph partitioning.     

The highly conserved spermatophyte cell wall DUF642 protein family: phylogeny and first evidence of interaction with cell wall polysaccharides in vitro

The evolution of spermatophyte plants involved fundamental changes in cell wall structure and function which resulted from diversification of carbohydrates and proteins. Cell wall proteomic analyses identified a novel family of proteins of yet unknown function, the DUF642 (Domain of Unknown Function 642) proteins. To investigate the evolution of the DUF642 gene family, 154 gene sequences from 24 plant species were analyzed, and phylogenetic inferences were conducted using the Maximum Likelihood and Bayesian Inference methods. Orthologous genes were detected in spermatophyte species and absent in non-seed known plant genomes. Protein sequences shared conserved motifs that defined the signature of the family. Distribution of conserved motifs indicated an ancestral intragenic duplication event. Gene phylogeny documented paleoduplication events originating three or four clades, depending on root position. When based on mid-point rooting, it retrieved four monophyletic clades: A, B, C, and D. A glycosylphosphatidylinositol (GPI)-anchor site and one or two galactose-binding domains-like (GBDLs) could be predicted for some DUF642 proteins. The B, C, and D clades grouped the predicted GPI-anchored proteins. First evidence of in vitro interaction of a DUF642 protein with a cell wall polysaccharide fraction is provided. A competition assay with cellulose prevented this interaction. The degree of diversification and the conservation of the family suggested that DUF642 proteins are key components in seed plant evolution.     

Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics

The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multilocus or "phylogenomic" data sets does not simply solve the problem, particularly when the data are analyzed with standard concatenation techniques. In our study, we conduct a phylogenetic study for a nearly complete species sample of the dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus, Microcebus) have been intensively studied over the past decade for reasons relating to their high level of cryptic species diversity, and although there has been emerging consensus regarding the evolutionary diversity contained within the genus, there is no agreement as to the inter-specific relationships within the group. We attempt to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multilocus data set. We compare the results of Bayesian concordance methods with those of standard gene concatenation, finding that though concatenation yields the strongest results as measured by statistical support, these results are found to be highly misleading. By employing an approach where individual alleles are treated as operational taxonomic units, we show that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process.     

Identification of a highly conserved domain on phytochrome from angiosperms to algae

A monoclonal antibody (Pea-25) directed to phytochrome from etiolated peas (Pisum sativum L., cv Alaska) binds to an antigenic domain that has been highly conserved throughout evolution. Antigenic cross-reactivity was evaluated by immunoblotting sodium dodecyl sulfate sample buffer extracts prepared from lyophilized tissue samples or freshly harvested algae. Pea-25 immunostained an approximately 120-kilodalton polypeptide from a variety of etiolated and green plant tissues, including both monocotyledons and dicotyledons. Moreover, Pea-25 immunostained a similarly sized polypeptide from the moss Physcomitrella, and from the algae Mougeotia, Mesotaenium, and Chlamydomonas. Because Pea-25 is directed to phytochrome, and because it stains a polypeptide about the size of oat phytochrome, it is likely that Pea-25 is detecting phytochrome in each case. The conserved domain that is recognized by Pea-25 is on the nonchromophore bearing, carboxyl half of phytochrome from etiolated oats. Identification of this highly conserved antigenic domain creates the potential to expand investigations of phytochrome at a cellular and molecular level to organisms, such as Chlamydomonas, that offer unique experimental advantages.     

Identification of putative multifunctional peptide synthetase genes using highly conserved oligonucleotide sequences derived from known synthetases

Many peptide antibiotics in prokaryotes and lower eukaryotes are produced non-ribosomally by multi-enzyme complexes. Analysis of gene-derived amino acid sequences of some peptide synthetases of bacterial and fungal origins revealed a high degree of conservation (35-50% identity). The genes encoding those peptide synthetases are clustered into large operons with repetitive domains (about 600 amino acids), in the case of synthetases activating more than one amino acid. We used two 35-mer oligonucleotides derived from two highly conserved regions of known peptide synthetases to identify the surfactin synthetase operon in Bacillus subtilis ATCC 21332, a strain not accessible to genetic manipulation. We show that the derived oligonucleotides can be used not only for the identification of unknown peptide synthetase genes by hybridization experiments but also in sequencing reactions as primers to identify internal domain sequences. Using this method, a 25.8-kb chromosomal DNA fragment bearing a part of the surfactin biosynthesis operon was cloned and partial sequences of two internal domains were obtained.     

Mitochondrial complex I from Arabidopsis and rice: orthologs of mammalian and fungal components coupled with plant-specific subunits

The NADH:ubiquinone oxidoreductase of the mitochondrial respiratory chain is a large multisubunit complex in eukaryotes containing 30-40 different subunits. Analysis of this complex using blue-native gel electrophoresis coupled to tandem mass spectrometry (MS) has identified a series of 30 different proteins from the model dicot plant, Arabidopsis, and 24 different proteins from the model monocot plant, rice. These proteins have been linked back to genes from plant genome sequencing and comparison of this dataset made with predicted orthologs of complex I components in these plants. This analysis reveals that plants contain the series of 14 highly conserved complex I subunits found in other eukaryotic and related prokaryotic enzymes and a small set of 9 proteins widely found in eukaryotic complexes. A significant number of the proteins present in bovine complex I but absent from fungal complex I are also absent from plant complex I and are not encoded in plant genomes. A series of plant-specific nuclear-encoded complex I associated subunits were identified, including a series of ferripyochelin-binding protein-like subunits and a range of small proteins of unknown function. This represents a post-genomic and large-scale analysis of complex I composition in higher plants.     

Mitochondrial complex I from Arabidopsis and rice: orthologs of mammalian and fungal components coupled with plant-specific subunits

The NADH:ubiquinone oxidoreductase of the mitochondrial respiratory chain is a large multisubunit complex in eukaryotes containing 30-40 different subunits. Analysis of this complex using blue-native gel electrophoresis coupled to tandem mass spectrometry (MS) has identified a series of 30 different proteins from the model dicot plant, Arabidopsis, and 24 different proteins from the model monocot plant, rice. These proteins have been linked back to genes from plant genome sequencing and comparison of this dataset made with predicted orthologs of complex I components in these plants. This analysis reveals that plants contain the series of 14 highly conserved complex I subunits found in other eukaryotic and related prokaryotic enzymes and a small set of 9 proteins widely found in eukaryotic complexes. A significant number of the proteins present in bovine complex I but absent from fungal complex I are also absent from plant complex I and are not encoded in plant genomes. A series of plant-specific nuclear-encoded complex I associated subunits were identified, including a series of ferripyochelin-binding protein-like subunits and a range of small proteins of unknown function. This represents a post-genomic and large-scale analysis of complex I composition in higher plants.