Direct maximum parsimony phylogeny reconstruction from genotype data

Background  

Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes.     

MLGO: phylogeny reconstruction and ancestral inference from gene-order data

Background

The rapid accumulation of whole-genome data has renewed interest in the study of using gene-order data for phylogenetic analyses and ancestral reconstruction. Current software and web servers typically do not support duplication and loss events along with rearrangements.

Results

MLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO is based on likelihood computation and shows advantages over existing methods in terms of accuracy, scalability and flexibility.

Conclusions

To the best of our knowledge, it is the first web tool for analysis of large-scale genomic changes including not only rearrangements but also gene insertions, deletions and duplications. The web tool is available from http://www.geneorder.org/server.php.     

Advances in Cambrian stratigraphy and paleontology: Integrating correlation techniques, paleobiology, taphonomy and paleoenvironmental reconstruction

Papers resulting from the Fourth International Symposium on the Cambrian System, held in Nanjing, China, in 2005 cover three major aspects of geology and paleontology: (1) the developing global standard for Cambrian chronostratigraphy or regional correlation schemes; (2) regional lithostratigraphy, sedimentology and paleoenvironments; (3) organismal paleobiology, phylogenetic affinities and taphonomy.A generalized curve of carbon isotopes (δ¹³C) through the Cambrian suggests a relationship between major biotic events, sea level history and the development of deposits of exceptional preservation (Lagerstätten). Recognition of this relationship increases the importance of the δ¹³C profile as a tool for intercontinental and intracontinental correlation. Significant δ¹³C excursions in the Cambrian are: BACE (negative excursion at the base of the Cambrian System); ZHUCE (positive excursion in the lower part of Stage 2); SHICE (negative excursion in the middle part of Stage 2); CARE (positive excursion near the base of Stage 3); MICE (positive excursion in the lower part of Stage 4); AECE (negative excursion in the middle part of Stage 4); ROECE (negative excursion near the base of Stage 5); DICE (negative excursion beginning near the base of the Drumian Stage); SPICE (positive excursion beginning at the base of the Paibian Stage); TOCE (negative excursion near the top of Stage 10). All acronyms other than SPICE are newly proposed.     

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

Background  

The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches.     

An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data

Background

Next-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. However, phylogenetic reconstruction of genomic data remains difficult because de novo assembly for non-model genomes and multi-genome alignment are challenging.

Results

To greatly simplify the analysis, we present an Assembly and Alignment-Free (AAF) method (https://sourceforge.net/projects/aaf-phylogeny) that constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment. Using mathematical calculations, models of sequence evolution, and simulated sequencing of published genomes, we address both evolutionary and sampling issues caused by direct reconstruction, including homoplasy, sequencing errors, and incomplete sequencing coverage. From these results, we calculate the statistical properties of the pairwise distances between genomes, allowing us to optimize parameter selection and perform bootstrapping. As a test case with real data, we successfully reconstructed the phylogeny of 12 mammals using raw sequencing reads. We also applied AAF to 21 tropical tree genome datasets with low coverage to demonstrate its effectiveness on non-model organisms.

Conclusion

Our AAF method opens up phylogenomics for species without an appropriate reference genome or high sequence coverage, and rapidly creates a phylogenetic framework for further analysis of genome structure and diversity among non-model organisms.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1647-5) contains supplementary material, which is available to authorized users.     

Squamate phylogeny, taxon sampling, and data congruence

To investigate the affinities of snakes, amphisbaenians and dibamids, the phylogenetic relationships among the major lineages (families) of extinct and extant squamates are assessed through a combined analysis of 248 osteological, 133 soft anatomical, and 18 ecological traits. The osteological data set represents a revision of previous data, taking into account recent criticism; the ecological data set is new. In addition, potentially critical fossil taxa (polyglyphanodontids and macrocephalosaurs) are included for the first time. The osteological and soft anatomical data sets each place snakes within anguimorphs, with dibamids and amphisbaenians near gekkotans. The putative primitive fossil amphisbaenian Sineoamphisbaena groups with macrocephalosaurs and polyglyphanodontids, together the sister group to scleroglossans. All three data sets are congruent, and these results are reinforced by combined analyses. In these, as in the osteological analyses, snakes are nested within marine lizards. However, exclusion of fossil taxa from the osteological data set results in a ‘limbless clade’ consisting of snakes, amphisbaenians and dibamids, and introduces significant conflict between osteology and soft anatomy. Also, deletion tests and character weighting reveal that the signal in the reduced osteological data set is internally contradictory. These results increase confidence in the arrangement supported by the all-taxon osteological, the soft anatomical, and the combined data, and suggest that exclusion of fossils confounds the signal in the osteological data set. Finally, the morphological data support the nesting of snakes within marine lizards, and thus a marine origin of snakes. This result still holds when relationships between living forms are constrained to the topology suggested by molecular sequences: if marine lizards are allowed to ‘float’ within this molecular framework, they form the stem group to snakes, and do not group with varanids as previously suggested.See also Electronic Supplement at: http://www.senckenberg.de/odes/05-04.htm.     

A distance measure based on binary character data and its application to phylogeny reconstruction

An essentially new method to relate a number of taxa on the basis of a predefined set of dichotomous properties (i.e. either present or not present) is described. The basic step of the analysis is the derivation of a sophisticated distance measure to describe the pairwise dissimilarities quantitatively on the basis of the individual properties. The presentation of the dissimilarity matrix by a tree-like structure is an obvious step implicated by the the distance measure and is related to the widely used method of successive joining of nearest neighbors with respect to the distances. The distance measure makes no use of stochastic or other mathematical models of evolutionary processes and can be interpreted best in terms of discrete information theory.     

Coding polymorphism for phylogeny reconstruction

The methodology of coding polymorphic taxa has received limited attention to date. A search of the taxonomic literature revealed seven types of coding methods. Apart from ignoring polymorphic characters (sometimes called the fixed-only method), two main categories can be distinguished: methods that identify the start of a new character state with the origin of an evolutionary novelty, and methods that identify the new state with the fixation of a novelty. The methods of the first category introduce soft reversals, yielding signals that support cladograms incompatible with true phylogenies. We conclude that coding the plesiomorphy is the method to be preferred, unless the ancestral state is unknown, in which case coding as ambiguous is recommended. This holds for coding polymorphism in species as well as in supraspecific taxa. In this light we remark on methods proposed by previous authors.     

The future of phylogeny reconstruction

A new approach to phylogenetic analysis, parsimony jackknifing, uses simple parsimony calculations combined with resampling of characters to arrive at a tree comprising well-supported groups. This is usually much the same as the consensus of most-parsimonious trees found from extensive multiple-tree calculations, but the new method is thousands of times faster, allowing analysis of much larger data matrices, and also provides information on the strength of support for different groups. Jackknife frequencies provide a more reliable assessment of support than do alternative methods, notably confidence probability (CP) and T-PTP testing.     

Detecting the node-density artifact in phylogeny reconstruction

The node-density effect is an artifact of phylogeny reconstruction that can cause branch lengths to be underestimated in areas of the tree with fewer taxa. Webster, Payne, and Pagel (2003, Science 301:478) introduced a statistical procedure (the "delta" test) to detect this artifact, and here we report the results of computer simulations that examine the test's performance. In a sample of 50,000 random data sets, we find that the delta test detects the artifact in 94.4% of cases in which it is present. When the artifact is not present (n = 10,000 simulated data sets) the test showed a type I error rate of approximately 1.69%, incorrectly reporting the artifact in 169 data sets. Three measures of tree shape or "balance" failed to predict the size of the node-density effect. This may reflect the relative homogeneity of our randomly generated topologies, but emphasizes that nearly any topology can suffer from the artifact, the effect not being confined only to highly unevenly sampled or otherwise imbalanced trees. The ability to screen phylogenies for the node-density artifact is important for phylogenetic inference and for researchers using phylogenetic trees to infer evolutionary processes, including their use in molecular clock dating.     

Simultaneous statistical multiple alignment and phylogeny reconstruction

Although the reconstruction of phylogenetic trees and the computation of multiple sequence alignments are highly interdependent, these two areas of research lead quite separate lives, the former often making use of stochastic modeling, whereas the latter normally does not. Despite the fact that reasonable insertion and deletion models for sequence pairs were already introduced more than 10 years ago, they have only recently been applied to multiple alignment and only in their simplest version. In this paper we present and discuss a strategy based on simulated annealing, which makes use of these models to infer a phylogenetic tree for a set of DNA or protein sequences together with the sequences'indel history, i.e., their multiple alignment augmented with information about the positioning of insertion and deletion events in the tree. Our method is also the first application of the TKF2 model in the context of multiple sequence alignment. We validate the method via simulations and illustrate it using a data set of primate mtDNA.     

New early Eocene anaptomorphine primate (Omomyidae) from the Washakie Basin,Wyoming, with comments on the phylogeny and paleobiology of anaptomorphines

Recent paleontological collecting in the Washakie Basin, southcentral Wyoming, has resulted in the recovery of over 100 specimens of omomyid primates from the lower Eocene Wasatch Formation. Much of what is known about anaptomorphine omomyids is based upon work in the Bighorn and Wind River Basins of Wyoming. This new sample documents greater taxonomic diversity of omomyids during the early Eocene and contributes to our understanding of the phylogeny and adaptations of some of these earliest North American primates. A new middle Wasatchian (Lysitean) anaptomorphine, Anemorhysis savagei, n. sp., is structurally intermediate between Teilhardina americana and other species of Anemorhysis and may be a sister group of other Anemorhysis and Trogolemur. Body size estimates for Anemorhysis, Tetonoides, Trogolemur, and Teilhardina americana indicate that these animals were extremely small, probably less than 50 grams. Analysis of relative shearing potential of lower molars of these taxa indicates that some were primarily insectivorous, some primarily frugivorous, and some may have been more mixed feeders. Anaptomorphines did not develop the extremes of molar specialization for frugivory or insectivory seen in extant prosimians. Incisor enlargement does not appear to be associated with specialization in either fruits or insects but may have been an adaptation for specialized grooming or food manipulation. © 1994 Wiley-Liss, Inc.     

Invariable sites models and their use in phylogeny reconstruction

Phylogenetic inference is well known to be problematic if both long and short branches occur together in the underlying tree. With biological data, correcting for this problem may require simultaneous consideration for both substitution biases and rate heterogeneity between lineages and across sequence positions. A particular form of the latter is the presence of invariable sites, which are well known to mislead estimation of genetic divergences. Here we describe a capture-recapture method to estimate the proportion of invariable sites in an alignment of amino acids or nucleotides. We use it to investigate phylogenetic signals in 18S ribosomal DNA sequences from Holometabolus insects. Our results suggest that, as taxa diverged, their 18S rDNA sequences have altered in both their distribution of sites that can vary as well as in their base compositions.     

Camouflage patterns in Nautilus, and their implications for cephalopod paleobiology

Cowen, R., Gertman, R. & Wiggett, Gail: Camouflage patterns in Nautilus , and their implications for cephalopod paleobiology.
Formal analysis of the pigment patterns of adult Nautilus shows that they are perfectly camouflaged for life in open water. But because of their accretionary growth pattern, juveniles are not fully camouflaged for open water: this supports previous suggestions that young Nautilus are benthonic. The principles of camouflage are used to re-assess some facets of cephalopod paleobiology. The life orientation of some early cyrtocones is re-interpreted. 'Ornament' on ammonoids is seen as camouflage structure, and we infer photic-nektonic, photic-benthonic, and aphotic habitats for three major morphological groups of ammonites. Sexual dimorphism in ammonites was probably accompanied by sexual separation in habitat, except for a short (annual) mating season. This is not inconsistent with modern cephalopod biology.     

Quartet-based phylogeny reconstruction with answer set programming

In this paper, a new representation is presented for the maximum quartet consistency (MQC) problem, where solving the MQC problem becomes searching for an ultrametric matrix that satisfies a maximum number of given quartet topologies. A number of structural properties of the MQC problem in this new representation are characterized through formulating into answer set programming, a recent powerful logic programming tool for modeling and solving search problems. Using these properties, a number of optimization techniques are proposed to speed up the search process. The experimental results on a number of simulated data sets suggest that the new representation, combined with answer set programming, presents a unique perspective to the MQC problem.     

The phylogeny of rotifers: molecular,ultrastructural and behavioural data

This work discusses the nature and significance of molecular, ultrastructural, and behavioural characters that can be used in phylogenetic analyses of rotifers.Recent molecular research has demonstrated the presence of very small amounts of 4-hydroxyproline in rotifers, probably arising from acetyl-cholinesterase or glycoproteins. Thus, rotifers appear to be the first known Metazoa without collagen.Ultrastructural work also has made some interesting discoveries. (1) The myelinic cuticle of the integument and pharynx of gastrotrichs is present in the pharynx of at least two rotifers (Philodina and Brachionus) and some Annelida. (2) The intracytoplasmic lamina (IL) of the syncytial ingestive integument of Acanthocephala is similar to the IL of the syncytial stomach of Bdelloidea. (3) The fibrous terminal web of primitive epidermal ciliated cells may have evolved in the skeletal IL of the syncytial, aciliated integument of rotifers. (4) Using the ultrastructural features of the skeletal, IL of the integument, I derived two possible dendograms of rotifer evolution. (5) These models and other ultrastructural data predict that Bdelloidea should be separated from Monogononta, while Seison has several characters which suggest that it should be more closely aligned to the Monogononta than previously proposed.Molecular and ultrastructural data suggest that rotifers are primitive Metazoa, probably derived by neoteny from ancestral, ciliated larvae. Finally, I argue that information on sensory organs and the behaviour of rotifers may offer unique insights into the evolution of the phylum.     

Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors

We report three developments toward resolving the challenge of the apparent basal polytomy of neoavian birds. First, we describe improved conditional down-weighting techniques to reduce noise relative to signal for deeper divergences and find increased agreement between data sets. Second, we present formulae for calculating the probabilities of finding predefined groupings in the optimal tree. Finally, we report a significant increase in data: nine new mitochondrial (mt) genomes (the dollarbird, New Zealand kingfisher, great potoo, Australian owlet-nightjar, white-tailed trogon, barn owl, a roadrunner [a ground cuckoo], New Zealand long-tailed cuckoo, and the peach-faced lovebird) and together they provide data for each of the six main groups of Neoaves proposed by Cracraft J (2001). We use his six main groups of modern birds as priors for evaluation of results. These include passerines, cuckoos, parrots, and three other groups termed "WoodKing" (woodpeckers/rollers/kingfishers), "SCA" (owls/potoos/owlet-nightjars/hummingbirds/swifts), and "Conglomerati." In general, the support is highly significant with just two exceptions, the owls move from the "SCA" group to the raptors, particularly accipitrids (buzzards/eagles) and the osprey, and the shorebirds may be an independent group from the rest of the "Conglomerati". Molecular dating mt genomes support a major diversification of at least 12 neoavian lineages in the Late Cretaceous. Our results form a basis for further testing with both nuclear-coding sequences and rare genomic changes.