Statistical method for estimating the standard errors of branch lengths in a phylogenetic tree reconstructed without assuming equal rates of nucleotide substitution among different lineages.

A statistical method is developed for estimating the standard errors of branch lengths in a phylogenetic tree reconstructed without assuming equal rates of nucleotide substitution among different lineages. This method can be easily used for testing whether the length of an interior branch in a reconstructed tree is positive, i.e., whether the topology of the tree is correct. Computer simulations indicate that this method is appropriate for a statistical test. As an example, this method is applied to phylogenetic trees reconstructed for the four hominoid species: human, chimpanzee, gorilla, and orangutan. The results obtained show that the present method provides a powerful statistical test.     

A conditional probability of reconstruction measure for internal cladogram branches

The conditional probability of reconstruction is a measure of the robustness of cladogram internodes and, unlike Bremer support and bootstrapping values, directly gauges probability. The new method compares the three putative branch lengths (the optimal and two alternatives) obtained through branch recalculation after nearest neighbor interchange and recalculation under constraint. With rooted trees, one switches the two free lineages attached at the distal end of an internal branch with the basal lineage. Probabilistic reconstruction of a branch for small data sets (e.g., morphological) is defined as having no contrary support for the two alternative branches and, when sufficient data are available (e.g., molecular studies), as meeting a selected confidence limit in chi-squared analysis. The exact probability that the internal branch is reconstructed is the same as the preselected confidence level met with chi-squared analysis; alternatively, it is a simple calculation of the length of the optimal branch divided by the sum of the lengths of all three putative branches. This new measure of robustness allows calculation of summary probabilities of subclade and tree reconstruction. The measure is conditional on a particular data set and optimization method but may also compare support from conflicting gene trees. Examples are provided by a morphological data set (the bryophyte Didymodon) and a molecular data set (primates).     

Lineages-through-time plots of neutral models for speciation

Drawing inferences about macroevolutionary processes from phylogenetic trees is a fundamental challenge in evolutionary biology. Understanding stochastic models for speciation is an essential step in solving this challenge. We consider a neutral class of stochastic models for speciation, the constant rate birth-death process. For trees with n extant species - which might be derived from bigger trees via random taxon sampling - we calculate the expected time of the kth speciation event (k=1,...,n-1). Further, for a tree with n extant species, we calculate the density and expectation for the number of lineages at any time between the origin of the process and the present. With the developed methods, expected lineages-through-time (LTT) plots can be drawn analytically. The effect of random taxon sampling on LTT plots is discussed.     

Cell lineage analysis of the mammalian female germline

Fundamental aspects of embryonic and post-natal development, including maintenance of the mammalian female germline, are largely unknown. Here we employ a retrospective, phylogenetic-based method for reconstructing cell lineage trees utilizing somatic mutations accumulated in microsatellites, to study female germline dynamics in mice. Reconstructed cell lineage trees can be used to estimate lineage relationships between different cell types, as well as cell depth (number of cell divisions since the zygote). We show that, in the reconstructed mouse cell lineage trees, oocytes form clusters that are separate from hematopoietic and mesenchymal stem cells, both in young and old mice, indicating that these populations belong to distinct lineages. Furthermore, while cumulus cells sampled from different ovarian follicles are distinctly clustered on the reconstructed trees, oocytes from the left and right ovaries are not, suggesting a mixing of their progenitor pools. We also observed an increase in oocyte depth with mouse age, which can be explained either by depth-guided selection of oocytes for ovulation or by post-natal renewal. Overall, our study sheds light on substantial novel aspects of female germline preservation and development.     

PHYLOGENIES WITHOUT FOSSILS

Phylogenies that are reconstructed without fossil material often contain approximate dates for lineage splitting. For example, particular nodes on molecular phylogenies may be dated by known geographic events that caused lineages to split, thereby calibrating a molecular clock that is used to date other nodes. On the one hand, such phylogenies contain no information about lineages that have become extinct. On the other hand, they do provide a potentially useful testing ground for ideas about evolutionary processes. Here we first ask what such reconstructed phylogenies should be expected to look like under a birth-death process in which the birth and death parameters of lineages remain constant through time. We show that it is possible to estimate both the birth and death rates of lineages from the reconstructed phylogenies, even though they contain no explicit information about extinct lineages. We also show how such phylogenies can reveal mass extinctions and how their characteristic footprint can be distinguished from similar ones produced by density-dependent cladogenesis.     

Contrasting responses of seedling and sapling densities to livestock density in the Mongolian forest-steppe

The past and present regeneration of Siberian larch (Larix sibirica) was studied in the forest-steppe of the Mongolian Altai, an area which has experienced an increase in annual mean temperature by 2.1 °C since 1940 and is subjected to grazing by mixed herds of livestock owned by pastoral nomads. Past regeneration was reconstructed from tree rings and present regeneration was analyzed by surveying seedlings, sapling-sized trees and the occurrence of viable larch seeds in the soil seed bank. Forest regeneration occurred throughout the twentieth and the early twenty-first centuries in the forest interiors, but ceased after the late 1970s at forest edges. The density of sapling-sized larch trees decreased with livestock density linearly in the interior and exponentially at the edge. Most sapling-sized trees had visible damage from livestock browsing, which also manifested in wood-anatomical anomalies. By contrast, the densities of 1- and 2-year old seedlings increased with livestock density at the forest edge, suggesting that seedlings in this habitat benefitted from the reduction in competition intensity due to livestock grazing. This relationship also suggests that larch seedlings, in contrast to sapling-sized trees, were avoided by the livestock, as otherwise removal by the herbivores should have counteracted the promotion due to reduced competition. Near-consistency of the correlations of total livestock and goat densities with sapling and seedling densities suggests that the control of larch regeneration is primarily a function of goat density, which have tripled in the Mongolian livestock during the past 20 years for economic reasons.     

Response of fine roots to an experimental gap in a boreal Picea abies forest

We examined the initial response of the quantity and distribution of fine roots to the creation of an experimental canopy gap with a diameter of 50 m in a mature managed Norway spruce forest. Under the canopy, the fine root length densities of trees, shrubs, and grasses and herbs were 3207, 707 and 2738 m m^–2, respectively. The fine root biomass of trees, shrubs, and grasses and herbs were 182, 47 and 52 g m^–2, respectively. Two growing seasons after gap creation hardly any fine tree roots were found in the middle part of the gap. The living tree roots in the gap edge zone were mainly located within a 5-m distance from the standing edge trees. The indices developed here to show the influence of trees on fine root lenght density clearly revealed the effect of the vicinity of living trees on fine root lenght density. The root densities of grasses, herbs and dwarf shrubs did not show a clear response to gap creation despite the increase of their foliage. Our results suggest that in boreal spruce forests a gap disturbance creates a distinct tree root gap and that the gap edge trees do not extend their root systems rapidly into the formed root gap.     

A simple feature representation vector for phylogenetic analysis of DNA sequences

In this study, a simple 4^k-dimension feature representation vector is proposed to reconstruct phylogenetic trees, where k is the length of a word. The vector is composed of elements which characterize the relative difference of biological sequence from sequence generated by an independent random process. In addition, the variance of a vector which is obtained by averaging every column of feature representation matrix is employed to determine appropriate word length. In our experiments, reliable results can always be generated when word length is <7 which appears to be of lower computational complexity. Phylogenetic trees of 24 transferrins and 48 Hepatitis E viruses reconstructed at word length 6 are in good agreements with previous study, it shows that our method is efficient and powerful.     

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees

ABSTRACT: BACKGROUND: A number of software packages are available to generate DNA multiple sequence alignments (MSAs) evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages). RESULTS: We present the first package designed to generate MSAs evolving under discrete-time Markov processes on phylogenetic trees, directly from probability substitution matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site), the algorithm produces DNA alignments of desired length. GenNon-h is publicly available for download. CONCLUSION: The software presented here is an efficient tool to generate DNA MSAs on a given phylogenetic tree. GenNon-h provides the user with the nonstationary or nonhomogeneous phylogenetic data that is well suited for testing complex biological hypotheses, exploring the limits of the reconstruction algorithms and their robustness to such models.     

Disk-covering, a fast-converging method for phylogenetic tree reconstruction.

The evolutionary history of a set of species is represented by a phylogenetic tree, which is a rooted, leaf-labeled tree, where internal nodes represent ancestral species and the leaves represent modern day species. Accurate (or even boundedly inaccurate) topology reconstructions of large and divergent trees from realistic length sequences have long been considered one of the major challenges in systematic biology. In this paper, we present a simple method, the Disk-Covering Method (DCM), which boosts the performance of base phylogenetic methods under various Markov models of evolution. We analyze the performance of DCM-boosted distance methods under the Jukes-Cantor Markov model of biomolecular sequence evolution, and prove that for almost all trees, polylogarithmic length sequences suffice for complete accuracy with high probability, while polynomial length sequences always suffice. We also provide an experimental study based upon simulating sequence evolution on model trees. This study confirms substantial reductions in error rates at realistic sequence lengths.     

A fast algorithm for computing geodesic distances in tree space

Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths is the length of the shortest path between them in the continuous tree space introduced by Billera, Holmes, and Vogtmann. This tree space provides a powerful tool for studying and comparing phylogenetic trees, both in exhibiting a natural distance measure and in providing a euclidean-like structure for solving optimization problems on trees. An important open problem is to find a polynomial time algorithm for finding geodesics in tree space. This paper gives such an algorithm, which starts with a simple initial path and moves through a series of successively shorter paths until the geodesic is attained.     

Maximum a posteriori probability assignment (MAP‐A): an optimality criterion for phylogenetic trees via weighting and dynamic programming

One of the most time‐consuming aspects of Bayesian posterior probability analysis in the analysis of phylogenetic trees is the use of Metropolis‐coupled Markov chain Monte Carlo (MC³) methods to determine relative posteriors and identify maximum a posteriori (MAP) trees. Here, analytical and numerical methods are presented to determine tree likelihoods that are integrated over edge‐length (and other parameter) distributions. Given topological (tree) priors (flat or otherwise), this allows for identification of the maximum posterior probability assignment (MAP‐A) of character states to non‐leaf tree vertices via dynamic programming. Using this form of posterior probability as an optimality criterion, tree space can be searched using standard trajectory techniques and heuristically optimal MAP‐A trees can be identified with considerable time savings over MC³. Example cases are presented using aligned and unaligned molecular sequences as well as combined molecular and anatomical data.     

Bionomics ofPhyllonorycter (Lepidoptera,Gracillariidae) onQuercus. II. Effects of ants

The effects of ants on a population ofPhyllonorycter leaf miners were observed in an oak chaparral on the Ishikari Coast. The density of ant nests was higher at the chaparral's edge than in the interior, while the density of mines was lower at the edge than in the interior. The effects of ant predation were examined in a comparison between treated ant-free trees and untreated ant-rich trees. Percentages of the torn mines observed were higher on the ant-rich trees than on the ant-free trees, whereas the mortality due to parasitoids was higher on the ant-free trees than on the ant-rich trees. This shows that ants greatly contributed to the mortality of leaf miners.     

Red-Headed Woodpecker Nest-Habitat Thresholds in Restored Savannas

Abstract: The red-headed woodpecker (Melanerpes erythrocephalus) is a widespread, adaptable species that continues to decline across North America. We examined stand, nest-tree, and cavity characteristics of red-headed woodpeckers in restored savannas within the Necedah National Wildlife Refuge, Wisconsin, USA, during 2002 and 2003. Based on availability, red-headed woodpeckers selected snags and trees with greater dead limb length. Red-headed woodpeckers nested in areas with greater basal area, cavity density, snag density, limb-tree density, and total dead limb length. Red-headed woodpeckers exhibited a decadent-tree threshold that was most accurately measured by the number of trees with dead limbs around (0.04 ha) nests. We found that the probability of a red-headed woodpecker nest being present greatly increased above the decadent-tree threshold. Woodland managers throughout the red-headed woodpecker's extensive breeding range can use our results and recommendations to guide decadent-tree retention for this species.     

Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited

The family Brassicaceae comprises 3710 species in 338 genera, 25 recently delimited tribes, and three major lineages based on phylogenetic results from the chloroplast gene ndhF. To assess the credibility of the lineages and newly delimited tribes, we sequenced an approximately 1.8-kb region of the nuclear phytochrome A (PHYA) gene for taxa previously sampled for the chloroplast gene ndhF. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the approximately unbiased (AU) test to compare phylogenetic results from PHYA with findings from ndhF. We also combined ndhF and PHYA data and used a Bayesian mixed model approach to infer phylogeny. PHYA and combined analyses recovered the same three large lineages as those recovered in ndhF trees, increasing confidence in these lineages. The combined tree confirms the monophyly of most of the recently delimited tribes (only Alysseae, Anchonieae, and Descurainieae are not monophyletic), while 13 of the 23 sampled tribes are monophyletic in PHYA trees. In addition to phylogenetic results, we documented the trichome branching morphology of species across the phylogeny and explored the evolution of different trichome morphologies using the AU test. Our results indicate that dendritic, medifixed, and stellate trichomes likely evolved independently several times in the Brassicaceae.     

Comparing and displaying phylogenetic trees using edge union networks

The general problem of representing collections of trees as a single graph has led to many tree summary techniques. Many consensus approaches take sets of trees (either inferred as separate gene trees or gleaned from the posterior of a Bayesian analysis) and produce a single “best” tree. In scenarios where horizontal gene transfer or hybridization are suspected, networks may be preferred, which allow for nodes to have two parents, representing the fusion of lineages. One such construct is the cluster union network (CUN), which is constructed using the union of all clusters in the input trees. The CUN has a number of mathematically desirable properties, but can also present edges not observed in the input trees. In this paper we define a new network construction, the edge union network (EUN), which displays edges if and only if they are contained in the input trees. We also demonstrate that this object can be constructed with polynomial time complexity given arbitrary phylogenetic input trees, and so can be used in conjunction with network analysis techniques for further phylogenetic hypothesis testing.     

Diversity of dry forest epiphytes along a gradient of human disturbance in the tropical Andes

Question: Disturbance effects on dry forest epiphytes are poorly known. How are epiphytic assemblages affected by different degrees of human disturbance, and what are the driving forces? Location: An inter‐Andean dry forest landscape at 2300 m elevation in northern Ecuador. Methods: We sampled epiphytic bryophytes and vascular plants on 100 trees of Acacia macracantha in five habitats: closed‐canopy mixed and pure acacia forest (old secondary), forest edge, young semi‐closed secondary woodland, and isolated trees in grassland. Results: Total species richness in forest edge habitats and on isolated trees was significantly lower than in closed forest types. Species density of vascular epiphytes (species per tree) did not differ significantly between habitat types. Species density of bryophytes, in contrast, was significantly lower in edge habitat and on isolated trees than in closed forest. Forest edge showed greater impoverishment than semi‐closed woodland and similar floristic affinity to isolated trees and to closed forest types. Assemblages were significantly nested; habitat types with major disturbance held only subsets of the closed forest assemblages, indicating a gradual reduction in niche availability. Distance to forest had no effect on species density of epiphytes on isolated trees, but species density was closely correlated with crown closure, a measure of canopy integrity. Main conclusions: Microclimatic changes but not dispersal constraints were key determinants of epiphyte assemblages following disturbance. Epiphytic cryptogams are sensitive indicators of microclimate and human disturbance in montane dry forests. The substantial impoverishment of edge habitat underlines the need for fragmentation studies on epiphytes elsewhere in the Tropics.     

New Analytic Results for Speciation Times in Neutral Models

In this paper, we investigate the standard Yule model, and a recently studied model of speciation and extinction, the “critical branching process.” We develop an analytic way—as opposed to the common simulation approach—for calculating the speciation times in a reconstructed phylogenetic tree. Simple expressions for the density and the moments of the speciation times are obtained. Methods for dating a speciation event become valuable, if for the reconstructed phylogenetic trees, no time scale is available. A missing time scale could be due to supertree methods, morphological data, or molecular data which violates the molecular clock. Our analytic approach is, in particular, useful for the model with extinction, since simulations of birth-death processes which are conditioned on obtaining n extant species today are quite delicate. Further, simulations are very time consuming for big n under both models.     

Estimating ancestral distributions of lineages with uncertain sister groups： a statistical approach to Dispersal-Vicariance Analysis and a case using Aesculus L. （Sapindaceae） including fossils

We propose a simple statistical approach for using Dispersal-Vicariance Analysis （DIVA） software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as P（rY） = ∑t^n=1 F（rY）t Pt where Y is a node, and F（rY） is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y, t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage ＂x＂, where x may vary due to phylogenetic uncertainty （polytomies and nodes with posterior probability 〈 100%）. Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes-DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp＊F（rY） on the Bayesian consensus tree when both variables are 〈 100%, where pp is the posterior probability and F（rY） is the frequency of range r for the node containing the specific crown group. We tested our DIVA-Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and ofAesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages. Additionally, we used the DIVA-Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the geographic