Reflecting its continuously increasing versatility and functionality, the popularity of the ape (analysis of phylogenetics and evolution) software package has grown steadily over the years. Among its ...features, it has a strong distance-based component allowing the user to compute distances from aligned DNA sequences based on most methods from the literature and also build phylogenetic trees from them. However, even data generated with modern genomic approaches can fail to give rise to sufficiently reliable distance estimates. One way to overcome this problem is to exclude such estimates from data analysis giving rise to an incomplete distance data set (as opposed to a complete one). So far their analysis has been out of reach for ape. To remedy this, we have incorporated into ape several methods from the literature for phylogenetic inference from incomplete distance matrices. In addition, we have also extended ape's repertoire for phylogenetic inference from complete distances, added a new object class to efficiently encode sets of splits of taxa, and extended the functionality of some of its existing functions.
ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/web/packages/ape/index.html Further information may be found at http://ape.mpl.ird.fr/pegas/
Acidobacteria constitute a globally widespread phylum and mainly inhabit soil environments. Despite their high abundance and activity, only 60 species from seven of the 26 acidobacterial subdivisions ...(sds; corresponding to class level) are (validly) described. Thus, only a low number of higher taxonomic ranks is currently distinguished within the Acidobacteria. Additionally, the distribution of the known acidobacterial species within the described families of the Acidobacteriaceae (sd1), Bryobacteraceae (sd3), Blastocatellaceae (sd4), Pyrinomonadaceae (sd4), Holophagaceae (sd8) and Acanthopleuribacteraceae (sd8) is extremely biased as most strains are affiliated with the Acidobacteriaceae. Members of this family are characteristic for acidic soils. In contrast, culture-independent analysis of microbial communities worldwide revealed that sd6 Acidobacteria prevail in soils with neutral pH. To improve the existing acidobacterial taxonomy, we here formally describe the first family within sd6 Acidobacteria, the Vicinamibacteraceae. Members of the Vicinamibacteraceae are aerobic, neutrophilic, psychrotolerant to mesophilic chemoheterotrophs. Their cells stain Gram-negative, do not form capsules or spores, and are non-motile. They occur as single cells or in aggregates and divide by binary fission. Growth occurs on sugars or complex proteinaceous compounds. MK-8 is the major quinone. Major fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C18 : 1ω7c or ω9c, iso-C17 : 1ω9c, C16 : 0 and iso-C17 : 0. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol are the major polar lipids. Unidentified glycolipids or unknown phospholipids might also be present. The G+C content of the DNA ranges from 64.7 to 65.9 mol%. Within the Vicinamibacteraceae fam. nov., Vicinamibacter and Luteitalea are the only genera described so far.
Convergent evolution is an important process in which independent species evolve similar features usually over a long period of time. It occurs with many different species across the tree of life, ...and is often caused by the fact that species have to adapt to similar environmental niches. In this paper, we introduce and study properties of a distance-based model for convergent evolution in which we assume that two ancestral species converge for a certain period of time within a collection of species that have otherwise evolved according to an evolutionary clock. Under these assumptions it follows that we obtain a distance on the collection that is a modification of an ultrametric distance arising from an equidistant phylogenetic tree. As well as characterising when this modified distance is a tree metric, we give conditions in terms of the model’s parameters for when it is still possible to recover the underlying tree and also its height, even in case the modified distance is not a tree metric.
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally ...generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks.
•Two new operations are introduced for transforming unrooted phylogenetic networks.•Any network can be transformed into any other network with the same size using NNI operations.•Any network can be transformed into any other using only two operations.•New connections between phylogenetic networks and cubic graphs are employed.•Novel spaces of networks arise which generalize phylogenetic tree space.
Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that ...is, a network with minimum hybrid number. Such networks are useful for representing the evolution of species whose genomes have undergone processes such as lateral gene transfer and recombination that cannot be represented appropriately by a phylogenetic tree. Even so, as was recently pointed out in the literature, insisting that a network displays the set of trees can be an overly restrictive assumption when modeling certain evolutionary phenomena such as incomplete lineage sorting. In this paper, we thus consider the less restrictive notion of rigidly displaying which we introduce and study here. More specifically, we characterize when two trees can be rigidly displayed by a certain type of phylogenetic network called a temporal tree-child network in terms of fork-picking sequences. These are sequences of special subconfigurations of the two trees related to the well-studied cherry-picking sequences. We also show that, in case it exists, the rigid hybrid number for two phylogenetic trees is given by a minimum weight fork-picking sequence for the trees. Finally, we consider the relationship between the rigid hybrid number and three closely related numbers; the weak, beaded, and temporal hybrid numbers. In particular, we show that these numbers can all be different even for a fixed pair of trees, and also present an infinite family of pairs of trees which demonstrates that the difference between the rigid hybrid number and the temporal-hybrid number for two phylogenetic trees on the same set of
n
leaves can grow at least linearly with
n
.
Tree reconciliation is the mathematical tool that is used to investigate the coevolution of organisms, such as hosts and parasites. A common approach to tree reconciliation involves specifying a ...model that assigns costs to certain events, such as cospeciation, and then tries to find a mapping between two specified phylogenetic trees which minimizes the total cost of the implied events. For such models, it has been shown that there may be a huge number of optimal solutions, or at least solutions that are close to optimal. It is therefore of interest to be able to systematically compare and visualize whole collections of reconciliations between a specified pair of trees. In this article, we consider various metrics on the set of all possible reconciliations between a pair of trees, some that have been defined before but also new metrics that we shall propose. We show that the diameter for the resulting spaces of reconciliations can in some cases be determined theoretically, information that we use to normalize and compare properties of the metrics. We also implement the metrics and compare their behavior on several host parasite data sets, including the shapes of their distributions. In addition, we show that in combination with multidimensional scaling, the metrics can be useful for visualizing large collections of reconciliations, much in the same way as phylogenetic tree metrics can be used to explore collections of phylogenetic trees. Implementations of the metrics can be downloaded from: https://team.inria.fr/erable/en/team-members/blerina-sinaimeri/reconciliation-distances/
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Members of the metabolically diverse order
inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. ...Cells of strains 0125_3
and Swamp67
are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome
-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3
and Swamp67
are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C
7
, C
and C
. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3
and Swamp67
was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3
were
ATCC 25196
,
FAM5
and
AcBE2-1
, while
ATCC 25196
,
Nv1
and
APG3
were closest to strain Swamp67
. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species
sp. nov (type strain 0125_3
=DSM 104443
=LMG 29998
=CECT 9241
) and
sp. nov. (type strain Swamp67
=DSM 104440
=LMG 29997
=CECT 9242
) of the novel genus
gen. nov., within the novel family
fam. nov.
Phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, ...clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i.e. uniquely describe) the network that induces it? For the large class of level-1 (phylogenetic) networks we characterize those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. In addition, we show that three known distance measures for comparing phylogenetic networks are in fact metrics on the resulting subclass and give the diameter for two of them. Finally, we investigate the related concept of indistinguishability and also show that many properties enjoyed by level-1 networks are not satisfied by networks of higher level.
Finite metric spaces are an essential tool in discrete mathematics and have applications in several areas including computational biology, image analysis, speech recognition, and information ...retrieval. Given any such metric D on a finite set X, an important problem is to find appropriate ways to realize D by weighting the edges in some graph G containing X in its vertex set such that D(x,y) equals the length of a shortest path from x to y in G for all x,y∈X. Here we focus on realizations with minimum total edge weight, called optimal realizations. By considering the 2-connected components and bridges in any optimal realization G of D we obtain an additive decomposition of D into simpler metrics. We show that this decomposition, called the block decomposition, is canonical in that it only depends on D and not on G, and that the decomposition can be computed in O(|X|3) time. As well as providing a fundamental new way to decompose any finite metric space, we expect that the block decomposition will provide a useful preprocessing tool for deriving metric realizations.
Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose ...non-leaf vertices are labeled by speciation or gene duplication events), and to then look for a species tree which can be reconciled with this tree through a
reconciliation map
between the trees. In practice, however, it can happen that there is no such map from a given event-labeled tree to
any
species tree. An important situation where this might arise is where the species evolution is better represented by a
network
instead of a tree. In this paper, we therefore consider the problem of reconciling event-labeled trees with species networks. In particular, we prove that any event-labeled gene tree can be reconciled with some network and that, under certain mild assumptions on the gene tree, the network can even be assumed to be multi-arc free. To prove this result, we show that we can always reconcile the gene tree with some multi-labeled (MUL-)tree, which can then be “folded up” to produce the desired reconciliation and network. In addition, we study the interplay between reconciliation maps from event-labeled gene trees to MUL-trees and networks. Our results could be useful for understanding how genomes have evolved after undergoing complex evolutionary events such as polyploidy.
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