Analyzing and reconstructing reticulation networks under timing constraints

Reticulation networks are now frequently used to model the history of life for various groups of species whose evolutionary past is likely to include reticulation events such as horizontal gene transfer or hybridization. However, the reconstructed networks are rarely guaranteed to be temporal. If a reticulation network is temporal, then it satisfies the two biologically motivated timing constraints of instantaneously occurring reticulation events and successively occurring speciation events. On the other hand, if a reticulation network is not temporal, it is always possible to make it temporal by adding a number of additional unsampled or extinct taxa. In the first half of the paper, we show that deciding whether a given number of additional taxa is sufficient to transform a non-temporal reticulation network into a temporal one is an NP-complete problem. As one is often given a set of gene trees instead of a network in the context of hybridization, this motivates the second half of the paper which provides an algorithm, called TemporalHybrid, for reconstructing a temporal hybridization network that simultaneously explains the ancestral history of two trees or indicates that no such network exists. We further derive two methods to decide whether or not a temporal hybridization network exists for two given trees and illustrate one of the methods on a grass data set.     

Hybrids in real time

We describe some new and recent results that allow for the analysis and representation of reticulate evolution by non-tree networks. In particular, we (1) present a simple result to show that, despite the presence of reticulation, there is always a well-defined underlying tree that corresponds to those parts of life that do not have a history of reticulation; (2) describe and apply new theory for determining the smallest number of hybridization events required to explain conflicting gene trees; and (3) present a new algorithm to determine whether an arbitrary rooted network can be realized by contemporaneous reticulation events. We illustrate these results with examples. [Directed acyclic graph; reticulate evolution; hybrid species; sub-tree prune and re-graft.].     

A decomposition theory for phylogenetic networks and incompatible characters.

Phylogenetic networks are models of evolution that go beyond trees, incorporating non-tree-like biological events such as recombination (or more generally reticulation), which occur either in a single species (meiotic recombination) or between species (reticulation due to lateral gene transfer and hybrid speciation). The central algorithmic problems are to reconstruct a plausible history of mutations and non-tree-like events, or to determine the minimum number of such events needed to derive a given set of binary sequences, allowing one mutation per site. Meiotic recombination, reticulation and recurrent mutation can cause conflict or incompatibility between pairs of sites (or characters) of the input. Previously, we used "conflict graphs" and "incompatibility graphs" to compute lower bounds on the minimum number of recombination nodes needed, and to efficiently solve constrained cases of the minimization problem. Those results exposed the structural and algorithmic importance of the non-trivial connected components of those two graphs. In this paper, we more fully develop the structural importance of non-trivial connected components of the incompatibility and conflict graphs, proving a general decomposition theorem (Gusfield and Bansal, 2005) for phylogenetic networks. The decomposition theorem depends only on the incompatibilities in the input sequences, and hence applies to many types of phylogenetic networks, and to any biological phenomena that causes pairwise incompatibilities. More generally, the proof of the decomposition theorem exposes a maximal embedded tree structure that exists in the network when the sequences cannot be derived on a perfect phylogenetic tree. This extends the theory of perfect phylogeny in a natural and important way. The proof is constructive and leads to a polynomial-time algorithm to find the unique underlying maximal tree structure. We next examine and fully solve the major open question from Gusfield and Bansal (2005): Is it true that for every input there must be a fully decomposed phylogenetic network that minimizes the number of recombination nodes used, over all phylogenetic networks for the input. We previously conjectured that the answer is yes. In this paper, we show that the answer in is no, both for the case that only single-crossover recombination is allowed, and also for the case that unbounded multiple-crossover recombination is allowed. The latter case also resolves a conjecture recently stated in (Huson and Klopper, 2007) in the context of reticulation networks. Although the conjecture from Gusfield and Bansal (2005) is disproved in general, we show that the answer to the conjecture is yes in several natural special cases, and establish necessary combinatorial structure that counterexamples to the conjecture must possess. We also show that counterexamples to the conjecture are rare (for the case of single-crossover recombination) in simulated data.     

Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable

Reticulation processes in evolution mean that the ancestral history of certain groups of present-day species is non-tree-like. These processes include hybridization, lateral gene transfer, and recombination. Despite the existence of reticulation, such events are relatively rare and so a fundamental problem for biologists is the following: Given a collection of rooted binary phylogenetic trees on sets of species that correctly represent the tree-like evolution of different parts of their genomes, what is the smallest number of "reticulation" vertices in any network that explains the evolution of the species under consideration? It has been previously shown that this problem is NP-hard even when the collection consists of only two rooted binary phylogenetic trees. However, in this paper, we show that the problem is fixed-parameter tractable in the two-tree instance, when parameterized by this smallest number of reticulation vertices.     

When two trees go to war

Rooted phylogenetic networks are used to model non-treelike evolutionary histories. Such networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate how they are related. Motivated by the parsimony principle, one often aims to construct a network that contains as few reticulations (non-treelike evolutionary events) as possible. In general, the model chosen influences the minimum number of reticulation events required. However, when one obtains the input data from two binary (i.e. fully resolved) trees, we show that the minimum number of reticulations is independent of the model. The number of reticulations necessary to represent the trees, triplets, clusters (in the softwired sense) and characters (with unrestricted multiple crossover recombination) are all equal. Furthermore, we show that these results also hold when not the number of reticulations but the level of the constructed network is minimised. We use these unification results to settle several computational complexity questions that have been open in the field for some time. We also give explicit examples to show that already for data obtained from three binary trees the models begin to diverge.     

Reconstructing reticulate evolution in species-theory and practice.

We present new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation; both methods are based upon extensions of Wayne Maddison's approach in his seminal 1997 paper. Our first method is a polynomial time algorithm for constructing phylogenetic networks from two gene trees contained inside the network.We allow the network to have an arbitrary number of reticulations, but we limit the reticulation in the network so that the cycles in the network are node-disjoint ("galled"). Our second method is a polynomial time algorithm for constructing networks with one reticulation, where we allow for errors in the estimated gene trees. Using simulations, we demonstrate improved performance of this method over both NeighborNet and Maddison's method.     

Parsimony Analysis as a Specific Kind of Homology Estimation and the Implications for Character Weighting

“Remane-Hennigian systematists” still reject parsimony analysis for phylogenetics, because homology or apomorphy analyses are not included. In contrast, “pattern cladists” regard homology as a deductive concept after applying a parsimony test of character congruence. However, as in molecular phylogeny, selection of “good” characters is always done on the basis of ana priorihomology analysis. The distribution criterion of homology—“homologous characters have identical or hierarchical distribution”—is the basis of parsimony analysis. Because this criterion also might fail in cases of genealogical reticulation or concerted homoplasy, character congruence is not a strict test but another probabilistic criterion of homology. A synthetic approach is proposed for phenotypic analysis with application ofa prioricriteria of homology. The resultinga prioriprobabilities of homology serve as criteria for selection and weighting of characters (very low = not selected/poor/mediocre/good/Dollo characters). After application of a parsimony algorithm the final cladogram decides homology estimations.     

Bootstrap-based Support of HGT Inferred by Maximum Parsimony

Background  

Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold.     

Phylogenetic Networks that Display a Tree Twice

In the last decade, the use of phylogenetic networks to analyze the evolution of species whose past is likely to include reticulation events, such as horizontal gene transfer or hybridization, has gained popularity among evolutionary biologists. Nevertheless, the evolution of a particular gene can generally be described without reticulation events and therefore be represented by a phylogenetic tree. While this is not in contrast to each other, it places emphasis on the necessity of algorithms that analyze and summarize the tree-like information that is contained in a phylogenetic network. We contribute to the toolbox of such algorithms by investigating the question of whether or not a phylogenetic network embeds a tree twice and give a quadratic-time algorithm to solve this problem for a class of networks that is more general than tree-child networks.     

Seasonal variations in the growth and amino acid pattern ofCaulerpa prolifera (Foerskal) Lamouroux

The amino acid pattern — free and bound — ofCaulerpa prolifera plants was studied. Maximum values for the total free amino acids were observed during periods of minimum growth, while minimum values occurred during periods of maximum growth of the alga. The bound amino acids showed a reverse trend.     

The structure of diversity within New World mitochondrial DNA haplogroups: implications for the prehistory of North America

The mitochondrial DNA haplogroups and hypervariable segment I (HVSI) sequences of 1,612 and 395 Native North Americans, respectively, were analyzed to identify major prehistoric population events in North America. Gene maps and spatial autocorrelation analyses suggest that populations with high frequencies of haplogroups A, B, and X experienced prehistoric population expansions in the North, Southwest, and Great Lakes region, respectively. Haplotype networks showing high levels of reticulation and high frequencies of nodal haplotypes support these results. The haplotype networks suggest the existence of additional founding lineages within haplogroups B and C; however, because of the hypervariability exhibited by the HVSI data set, similar haplotypes exhibited in Asia and America could be due to convergence rather than common ancestry. The hypervariability and reticulation preclude the use of estimates of genetic diversity within haplogroups to argue for the number of migrations to the Americas.     

TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets

The problem of constructing an optimal rooted phylogenetic network from an arbitrary set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet, which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from an arbitrary set of rooted triplets. Despite of current methods that work for dense set of rooted triplets, a key innovation is the applicability of TripNet to non-dense set of rooted triplets. We prove some theorems to clarify the performance of the algorithm. To demonstrate the efficiency of TripNet, we compared TripNet with SIMPLISTIC. It is the only available software which has the ability to return some rooted phylogenetic network consistent with a given dense set of rooted triplets. But the results show that for complex networks with high levels, the SIMPLISTIC running time increased abruptly. However in all cases TripNet outputs an appropriate rooted phylogenetic network in an acceptable time. Also we tetsed TripNet on the Yeast data. The results show that Both TripNet and optimal networks have the same clustering and TripNet produced a level-3 network which contains only one more reticulation node than the optimal network.     

Electrical processes involved in the encoding of nerve impulses

A mechanism for impulse encoding is advanced for those neurones whose impulse trigger zone membrane is more excitable than the general axonal membrane. Electrical communication between an electrotonically small patch of highly excitable membrane and neighboring membrane places the control of membrane potential — in varying degree — to the larger membrane area throughout the interspike intervals. That control is relinquished to the trigger membrane near the time of action potential initiation in a natural fashion. Model calculations demonstrate that this mechanism can lead to a dramatic lowering of the minimum stable firing frequency of tonic neurons, and, additionally influence the shape of the stimulus —versus — impulse frequency curve. The results are compared with the behavior of the slowly adapting stretch receptor neuron of the crayfish.Research supported by NSF grant BNS 77-22532 and Public Health Service Grant EY 00293. Computer facilities were made available by the Air Force Office of Scientific Research (AFOSR-1221) and by the University of Minnesota Computer Center     

The microwave Rio-Hortega technique: a 24 hour method

Summary Application of microwaves in histochemistry and cytochemistry generally speeds up the technique. Microwaves stimulate diffusion into the tissue and influence the proteins and membrane of the cell. Silver impregnation techniques for the brain, such as the fast Rio—Hortega or the slow Golgi—Cox technique, normally require a minimum time period of 7 days and 20 days respectively. Using microwaves, the Rio—Hortega technique can be completed within 24 h. In sections prepared from mature brains, good silver impregnation of cell bodies, of axons and their terminals, and of dendrites and their spines are obtained. An explanation is given as to why the method cannot be further reduced in time. To our knowledge, this is the first report of the application of microwave irradiation for colouring pieces of tissue.     

New electron-capture gas-liquid chromatographic method for the determination of mexiletine plasma levels in man

A method for the determination of mexiletine in human plasma by gas—liquid chromatography with electron-capture detection is described. Plasma samples are extracted at pH 12 with dichloromethane after addition of the internal standard, the 2,4-methyl analogue of mexiletine. A derivative is obtained using heptafluorobutyric anhydride; according to gas chromatography—mass spectrometry it is a monoheptafluorobutyryl compound. The minimum detectable amount of mexiletine is 5 pg. Accurate determinations of human plasma levels were performed after oral or intravenous treatment.     

Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae)

A parsimony analysis of 133 sequences of the nuclear ribosomal DNA ITS1 + 5.8S + ITS2 region from 71 taxa in Armeria was carried out. The presence of additive polymorphic sites (APS; occurring in 14 accessions) fits the reticulate scenario proposed in previous work for explaining the ITS pattern of variation on a much smaller scale and is based mainly on the geographical structure of the data, irrespective of taxonomic boundaries. Despite the relatively low bootstrap values and large polytomies, part of which are likely due to disruptive effects of reticulation and concerted evolution in these multicopy sequences, the ITS analysis has phylogenetic and biogeographic implications. APS detected in this study are consistent with hypothesized hybridization events, although biased concerted evolution, previously documented in the genus, needs to be invoked for specific cases and may be responsible for a possible “sink” effect in terminals from a large clade. The causes for sequences of the same species appearing in different clades (here termed transclade) are discussed.     

Orangutan Home Range Size and Its Determinants in a Sumatran Swamp Forest

Orangutans (Pongo pygmaeus) in a Sumatran swamp forest used home ranges far larger than any described so far for the species, in spite of living at the highest density on record. Although it was difficult to estimate home range sizes, minimum reliably estimated home range sizes for adult females are ca. 850 ha, whereas subadult and adult males used ranges of at least ca. 2500 ha, and perhaps much more. Range overlap was very high: up to 16 adult females, 9 adult males and at least 15 subadult males were seen within a single 4-ha square in the center of the study area. We found no evidence for the use of seasonally distincthome ranges—commuters—, and only some subadult males may have been transients—wanderers—without a stable home range. The large size of the home ranges is attributed to the coarse grain of the habitat mosaic, with orangutans converging on parts with a high density of favored fruit trees. Orangutans at this swamp forest included a variety of habitat types within their ranges.     

Hypergastrinaemia induced by acid blockade evokes enterochromaffin-like (ECL) cell hyperplasia in chicken,hamster and guinea-pig stomach

Summary Treatment of chickens, hamsters and guinea-pigs with large doses of the long-acting antisecretory agent omeprazole for 10 weeks resulted in elevated serum gastrin levels and in increased stomach weight and mass of oxyntic mucosa. Also the antral gastrin cell density was increased. Another striking effect was the hyperplasia of the histamine-producing enterochromaffin-like (ECL) cells — a prominent endocrine cell population with unknown function — in the oxyntic mucosa. Accordingly, the gastric mucosal histamine concentration and rate of histamine formation were increased in all three species. The results suggest that marked and long-lasting suppression of acid secretion leads to elevated serum gastrin levels and diffuse ECL cell hyperplasia not only in the rat, as previously seen, but also in the chicken, hamster and guinea-pig; this hyperplasia is associated with accelerated histamine formation in all three species. The following sequence of events is suggested to occur in mammalian as well as submammalian vertebrates: suppression of acid secretion — hypergastrinaemia — ECL cell hyperplasia.     

Predator Mobbing in <Emphasis Type="Italic">Tarsius spectrum</Emphasis>

Whereas most animals make considerable effort to avoid their predators, numerous species tend to approach and to confront predators as a group: mobbing. Among the types of predators that elicit mobbing, snakes seem to be one of the more consistent recipients of it. I describe the mobbing behavior of spectral tarsiers toward live and model snakes. In particular, I explore individual differences—sex, age and reproductive status—in mobbing behavior at Tangkoko Nature Reserve, Sulawesi, Indonesia. In 1994–1995, I observed 11 groups for 18 mo, and in 1999, I observed 9 groups for 6 mo. Over all I recorded, 11 natural mobbing events and 9 artificially induced mobbing events. The mean number of individuals at a natural mobbing is 5.1 with an average duration of 33 min. The duration of a mobbing event is strongly correlated with the number of mobbers. Adults were more likely than other age classes to participate in mobbings. Males were more likely than females to participate in mobbings. Mobbing groups often contained > 1 adult male despite the fact that no spectral tarsier group contains > 1 adult male. Vis-à-vis Curios (1978) 9 hypotheses for the function of mobbing suggests that its primary function in spectral tarsiers may be perception advertisement or teaching snakes to move on.     

Biopolymer particulate turnover in biological waste treatment systems: a review

Microorganisms — the major component in most biological waste treatment processes and a number of industrial fermentations — are not able to directly assimilate biopolymeric particulate material. Such organic particulates must first be solubilized into soluble polymers or monomers before they can diffuse through the capsular slime layer surrounding most bacteria, then transported across the cell membrane, to be used as either a carbon, energy or other essential nutrient source. Throughout these events, new cells are synthesized, which are themselves biopolymer particulates.The turnover of biopolymer particulates in biological treatment systems has not been examined with respect to its impact on system performance and culture physiology. The aim of this paper is to review the observations of particulate turnover in various biological treatment systems and to identify those fundamental mechanisms which govern microbial conversion of biopolymer particulates.Current address: Department of Chemical Engineering, California, Institute of Technology, Pasadena, Ca 91125 USA