Trait-dependent extinction leads to greater expected biodiversity loss (2009)
We use a classical combinatorial inequality to establish a Markov inequality for multivariate binary Markov processes on trees. We then apply this result, alongside with the FKG inequality, to...
Quantifying the Extent of Lateral Gene Transfer Required to Avert a `Genome of Eden' (2009)
Van Iersel, Leo, Semple, Charles, Steel, Mike
The complex pattern of presence and absence of many genes across different species provides tantalising clues as to how genes evolved through the processes of gene genesis, gene loss and lateral gene...
Expected length of pendant and interior edges of a Yule tree (2009)
The Yule (pure-birth) model is the simplest null model of speciation; each lineage gives rise to a new lineage independently with the same rate $\lambda$. We investigate the expected length of an...
Species, Clusters and the 'Tree of Life': A graph-theoretic perspective (2009)
Dress, Andreas, Moulton, Vincent, Steel, Mike, Wu, Taoyang
A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a...
Characterizing phylogenetically decisive taxon coverage (2009)
Steel, Mike, Sanderson, Michael J.
Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we...
A Hall-type theorem for triplet set systems based on medians in trees (2009)
Given a collection $\C$ of subsets of a finite set $X$, let $\bigcup \C = \cup_{S \in \C}S$. Philip Hall's celebrated theorem \cite{hall} concerning `systems of distinct representatives' tells us...
An improved bound on the Maximum Agreement Subtree problem (2009)
We improve the lower bound on the extremal version of the Maximum Agreement Subtree problem. Namely we prove that two binary trees on the same $n$ leaves have subtrees with the same $\geq c\log\log...
Unicyclic networks: compatibility and enumeration (2008)
Abstract—Graphs obtained from a binary leaf labeled (“phylogenetic”) tree by adding an edge so as to introduce a cycle provide a useful representation of hybrid evolution in molecular...
Expected Anomalies in the Fossil Record (2008)
Abstract: The problem of intermediates in the fossil record has been frequently discussed ever since Darwin. The extent of ‘gaps ’ (missing transitional stages) has been used to argue against...
Guoliang Li, Mike Steel, Louxin Zhang
Ancestral state reconstruction is an important approach to understanding the origins and evolution of key features of different living organisms (Liberles, 2007). For example, ancestral proteins and...
Mike Steel, Aki Mimoto, Arne Ø. Mooers
Abstract: If predictions for species extinctions hold, then the ‘tree of life ’ today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species...
Computing the Distribution of a Tree Metric (2008)
The Robinson-Foulds (RF) distance is by far the most widely used measure of dissimilarity between trees. Although the distribution of these distances has been investigated for twenty years, an...
A basic limitation on inferring phylogenies by pairwise sequence comparisons (2008)
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in...
Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny (2008)
Tanja Gernhard, Daniel Ford, Rutger Vos, Mike Steel
Abstract: The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a diffi cult question for biologists...
Phylogenetic information complexity: Is testing a tree easier than finding it? (2008)
Steel, Mike, Szekely, Laszlo, Mossel, Elchanan
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we...
Sequence length bounds for resolving a deep phylogenetic divergence (2008)
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are...
Markovian log-supermodularity, and its applications in phylogenetics (2008)
We establish a log-supermodularity property for probability distributions on binary patterns observed at the tips of a tree that are generated under any 2--state Markov process. We illustrate the...
OPTIMIZING PHYLOGENETIC DIVERSITY UNDER CONSTRAINTS (2008)
Vincent Moulton, Charles Semple, Mike Steel
Abstract. Phylogenetic diversity (PD) is a measure of the extent to which different subsets of taxa span an evolutionary tree, and provides a quantitative tool for studying biodiversity conservation....
Unicyclic networks: compatibility and enumeration (2008)
Abstract. Graphs obtained from a binary leaf labelled (‘phyloge-netic’) tree by adding an edge so as to introduce a cycle provide a useful representation of hybrid evolution in molecular...
Identifying X-Trees with Few Characters (2008)
Magnus Bordewich, Charles Semple, Mike Steel
Previous work has shown the perhaps surprising result that, for any binary phylogenetic tree T, there is a set of four characters that define T. Here we deal with the general case, where T is an...
Shrinkage Effect in Ancestral Maximum Likelihood (2008)
Mossel, Elchanan, Roch, Sebastien, Steel, Mike
Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral...
0 Applied Probability Trust 19% FOR THE PARSIMONY (2008)
In phylogenetic analysis it is useful to study the distribution of the parsimony length of a tree under the null model, by which the leaves are independently assigned letters according to prescribed...
Identifying X-Trees with Few Characters (2008)
Magnus Bordewich, Charles Semple, Mike Steel
Previous work has shown the perhaps surprising result that, for any binary phylogenetic tree T, there is a set of four characters that define T. Here we deal with the general case, where T is an...
Expected Anomalies in the Fossil Record (2008)
The problem of intermediates in the fossil record has been frequently discussed ever since Darwin. The extent of ‘gaps’ (missing transitional stages) has been used to argue against gradual...
Author’s Affiliations MIKE STEEL: Maximum Likelihood Supertrees (2008)
Mike Steel, Allen Rodrigo, Allen Rodrigo
consistency
Shrinkage Effect in Ancestral Maximum Likelihood (2008)
Elchanan Mossel, Sebastien Roch, Mike Steel
Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral...
Whitianga, New Zealand Whitianga ‘08 NEW ZEALAND PHYLOGENETICS CONFERENCE Participants (2008)
John Beck, David Bryant, Michael Charleston, Alan Cooper, Beata Faller, Mareike Fischer, ...
revisited
Distribution of phylogenetic diversity under random extinction (2008)
Beáta Faller, Fabio Pardi, Mike Steel
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the unknown subset of current species that will still be...
PLEASE SCROLL DOWN FOR ARTICLE (2008)
Publisher Taylor, Guoliang Li, Mike Steel, Louxin Zhang, Guoliang Li, Mike Steel, ...
This article may be used for research, teaching and private study purposes. Any substantial or systematic reproduction, re-distribution, re-selling, loan or sub-licensing, systematic supply or...
PHYLOGENETIC INFORMATION COMPLEXITY: IS TESTING A TREE EASIER THAN FINDING IT? (2008)
Mike Steel, Laszlo Székely, Elchanan Mossel, Mike Steel, Mike Steel, Laszlo Székely, ...
Abstract. Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In...
A regular decomposition of the edge-product space of phylogenetic trees (2008)
Gill, Jonna, Linusson, Svante, Moulton, Vincent, Steel, Mike
We investigate the topology and combinatorics of a topological space called the edge-product space that is generated by the set of edge-weighted finite labelled trees. This space arises by...
Maximum Likelihood Supertrees (2008)
We analyze a maximum likelihood approach for combining phylogenetic trees into a larger “supertree.” This is based on a simple exponential model of phylogenetic error, which ensures that ML...
Gruenheit, Nicole, Lockhart, Peter J., Steel, Mike, Martin, William
The covarion (COV)-like properties of sequences are poorly described and their impact on phylogenetic analyses poorly understood. We demonstrate using simulations that, under an evolutionary model...
Simple But Fundamental Limitations on Supertree and Consensus Tree Methods (2007)
Introduction A fundamental problem in biological classification is the question of how best to combine into one phylogenetic tree a collection of phylogenetic trees that classify the same or...
1 2 CHARLES SEMPLE AND MIKE STEEL Running Head: Group-valued tree proximities (2007)
Charles Semple, Mike Steel, Correspondence Charles Semple
Key words and phrases. Trees, groups, four-point condition, symbolic ultrametric. This work was supported by the New Zealand Marsden Fund (UOC-MIS-003).
Abstract. The reconstruction of evolutionary trees (phylogenies) from DNA sequence data is a central problem in biology. We describe simple sufficient conditions for two tree reconstruction methods...
Meei Pyng Ng, Mike Steel, Nicholas C. Wormald
difficulty of constructing a leaf-labelled tree including
between maximum likelihood and maximum parsimony
and consensus tree methods (2007)
Simple but fundamental limitations on supertree
Algorithmic aspects of tree (2007)
Sebastian Böcker, Gk Strukturbildungsprozesse, Fsp Mathematisierung, David Bryant, ...
‡ Mike Steel thanks the New Zealand Marsden Fund (UOC-MIS-003) for supporting this research 1 2 BÖCKER, BRYANT, DRESS, STEEL Proposed running head: Tree amalgamation
Syst. Biol. 53(2):327--332, 2004 (2007)
Copyright Society Of, Daniel H. Huson, Mike Steel
Given a collection of discrete characters (e.g., aligned DNA sites, gene adjacencies), a common measure of distance between taxa is the proportion of characters for which taxa have different...
Mike Steel, Daniel Huson, Peter J. Lockhart
Abstract.—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...
Maximum Likelihood Supertrees (2007)
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML...
Distribution of phylogenetic diversity under random extinction (2007)
Faller, Beata, Pardi, Fabio, Steel, Mike
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still...
Expected Anomalies in the Fossil Record (2007)
The problem of intermediates in the fossil record has been frequently discussed ever since Darwin. The extent of `gaps' (missing transitional stages) has been used to argue against gradual evolution...
Reconstructing pedigrees: a stochastic perspective (2007)
Thatte, Bhalchandra D., Steel, Mike
A pedigree is a directed graph that describes how individuals are related through ancestry in a sexually-reproducing population. In this paper we explore the question of whether one can reconstruct a...
Mixed-up trees: the structure of phylogenetic mixtures (2007)
Matsen, Frederick A., Mossel, Elchanan, Steel, Mike
In this paper we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture...
Hedging our bets: the expected contribution of species to future phylogenetic diversity (2007)
Steel, Mike, Mimoto, Aki, Mooers, Arne O.
If predictions for species extinctions hold, then the `tree of life' today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species is likely to...
Phylogenetic mixtures on a single tree can mimic a tree of another topology (2007)
Matsen, Frederick A., Steel, Mike
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture...
Hedging Our Bets: The Expected Contribution of Species to Future Phylogenetic Diversity (2007)
Mike Steel, Aki Mimoto, Arne Ø. Mooers
If predictions for species extinctions hold, then the ‘tree of life’ today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species is likely...
Allan Wilson Centre for Molecular Ecology and Evolution Corresponding author: (2007)
Mike Steel, Frederick A. Matsen, Mike Steel
1 The ‘star paradox ’ in phylogenetics is the tendency for a particular resolved tree to be sometimes strongly supported even when the data is generated by an unresolved (‘star’) tree. There...
A pedigree is a directed graph that describes how individuals are related through ancestry in a sexually-reproducing population. In this paper we explore the question of whether one can reconstruct a...
Frederick A. Matsen, Mike Steel
Abstract.—Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data are generated...
The Bayesian 'Star Paradox' Persists for Long Finite Sequences (2007)
Steel, Mike, Matsen, Frederick A.
The ‘star paradox’ in phylogenetics is the tendency for a particular resolved tree to be sometimes strongly supported even when the data is generated by an unresolved (‘star’) tree. There...
Phylogenetic Mixtures on a Single Tree Can Mimic a Tree of Another Topology (2007)
Matsen, Frederick A., Steel, Mike
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data are generated by a...
The Bayesian `star paradox' persists for long finite sequences (2006)
Steel, Mike, Matsen, Frederick A.
The `star paradox' in phylogenetics is the tendency for a particular resolved tree to be sometimes strongly supported even when the data is generated by an unresolved (`star') tree. There have been...
Estimating the relative order of speciation or coalescence events on a given phylogeny (2006)
Gernhard, Tanja, Ford, Daniel, Vos, Rutger, Steel, Mike
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can...
Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny (2006)
Tanja Gernhard, Daniel Ford, Rutger Vos, Mike Steel
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists– how can...
Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny (2006)
Tanja Gernhard, Daniel Ford, Rutger Vos, Mike Steel
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists– how can...
Abstract Closure operations in phylogenetics (2006)
Stefan Grünewald, Mike Steel, M. Shel Swenson
Closure operations are a useful device in both the theory and practice of tree reconstruction in biology and other areas of classification. These operations take a collection of trees (rooted or...
Abstract.—The Noah’s Ark Problem (NAP) is a comprehensive cost-effectiveness methodology for biodiversity conservation that was introduced by Weitzman (1998) and utilizes the phylogenetic tree...
Neighbor-Joining Revealed (2006)
It is nearly 20 years since the landmark paper (Saitou and Nei 1987) in Molecular Biology and Evolution introducing Neighbor-Joining (NJ). The method has become the most widely used method for...
Neighbor-Joining Revealed (2006)
It is nearly 20 years since the landmark paper (Saitou and Nei, 1987) in MBE introducing Neighbor-Joining (NJ). The method has become the most widely-used method for building phylogenetic trees from...
Baroni, Mihaela, Semple, Charles, Steel, Mike
We describe some new and recent results that allow for the analysis and representation of reticulate evolution by nontree networks. In particular, we (1) present a simple result to show that, despite...
The Noah's Ark Problem (NAP) is a comprehensive cost-effectiveness methodology for biodiversity conservation that was introduced by Weitzman (1998) and utilizes the phylogenetic tree containing the...
M.: Four characters suffice to convexly define a phylogenetic tree (2005)
Katharina T. Huber, Vincent Moulton, Mike Steel
Abstract. It was recently shown that just five characters (functions on a finite set X) suffice to convexly define a trivalent tree with leaf set X. Here we show that four characters suffice which,...
Annals of Combinatorics Phylogenetic Diversity Over an Abelian Group (2005)
AMS Subject Classification: 05C05, 92D15 Abstract. There is a natural way to associate to any tree T with leaf set X, and with edges weighted by elements from an abelian group G, a map from the power...
Phylogenetic Diversity and the Greedy Algorithm (2005)
Given a phylogenetic tree with leaves labeled by a collection of species, and with weighted edges, the “phylogenetic diversity” of any subset of the species is the sum of the edge weights of the...
Phylogenetic Diversity and the Greedy Algorithm (2005)
Given a phylogenetic tree with leaves labeled by a collection of species, and with weighted edges, the “phylogenetic diversity” of any subset of the species is the sum of the edge weights of the...
Random autocatalytic networks (2004)
We determine conditions under which a random biochemical system is likely to contain a subsystem that is both autocatalytic and able to survive on some ambient `food' source. Such systems have...
How much can evolved characters tell us about the tree that generated them? (2004)
In this paper we review some recent results that shed light on a fundamental question in molecular systematics: how much phylogenetic `signal' can we expect from characters that have evolved under...
Two further links between MP and ML under the Poisson model (2004)
Abstract. Maximum parsimony and maximum likelihood are two contrasting approaches for reconstructing phylogenetic trees from sequence and character data. We establish analytic links between these...
Phylogenetic trees based on gene content (2004)
Abstract. Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper we derive a maximum likelihood estimation of evolutionary distance...
Supertree algorithms for ancestral divergence dates and nested taxa. Bioinformatics (2004)
Charles Semple, Philip Daniel, Wim Hordijk, Mike Steel
Abstract. Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the `Tree of Life'. However, a limitation of such methods is that, typically,...
Accumulation Phylogenies (2004)
Abstract. Directed acyclic graphs provide a convenient representation of reticulate evolution in systematic biology. In this paper we formalize and analyse a simple model in which evolved...
Cyclic Permutations and Evolutionary Trees (2004)
Given a tree T with leaf set X, there are certain ways of arranging the elements of X in a circular order so that T can be embedded in the plane and `preserve' this ordering. We investigate some...
A Phase Transition for a Random Cluster Model on Phylogenetic Trees (2004)
We investigate a simple model that generates random partitions of the leaf set of a tree. Of particular interest is the reconstruction question: what number k of independent samples (partitions) are...
Supertree algorithms for ancestral divergence dates and nested taxa. Bioinformatics (2004)
Charles Semple, Philip Daniel, Wim Hordijk, Mike Steel
Abstract. Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the ‘Tree of Life’. However, a limitation of such methods is that, typically,...
Supertree algorithms for ancestral divergence dates and nested taxa. Bioinformatics (2004)
Charles Semple, Philip Daniel, Wim Hordijk, Mike Steel
Abstract. Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the ‘Tree of Life’. However, a limitation of such methods is that, typically,...
Supertree methods for ancestral divergence dates and other applications (2004)
David Bryant, Charles Semple, Mike Steel
Abstract: There are many ways to combine rooted phylogenetic trees with overlapping leaf sets into a single “supertree”. The most widely used method is MRP (matrix representation with parsimony...
Phylogenetic trees based on gene content (2004)
Summary: Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper, we derive a maximum-likelihood estimation of evolutionary distance...
Phylogenetic trees based on gene content (2004)
Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper we derive a maximum likelihood estimation of evolutionary distance between species...
Supertree algorithms for ancestral divergence dates and nested taxa (2004)
Semple, Charles, Daniel, Philip, Hordijk, Wim, Page, Roderic D. M., Steel, Mike
Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the ‘Tree of Life’. However, a limitation of such methods is that, typically, they use...
Phylogenetic trees based on gene content (2004)
Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper we derive a maximum likelihood estimation of evolutionary distance between species...
Supertree algorithms for ancestral divergence dates and nested taxa (2004)
Semple, Charles, Daniel, Philip, Hordijk, Wim, Page, Roderic D. M., Steel, Mike
Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the ‘Tree of Life’. However, a limitation of such methods is that, typically, they use...
Distances that Perfectly Mislead (2004)
Given a collection of discrete characters (e.g., aligned DNA sites, gene adjacencies), a common measure of distance between taxa is the proportion of characters for which taxa have different...
The ability of systems of molecular reactions to be simultaneously autocatalylic and sustained by some ambient ‘food source ’ of simple molecules may have been an essential step in the origin of...
Annals of Combinatorics A Framework for Representing Reticulate Evolution ∗ (2003)
Mihaela Baroni, Charles Semple, Mike Steel
Abstract. Acyclic directed graphs (ADGs) are increasingly being viewed as more appropriate for representing certain evolutionary relationships, particularly in biology, than rooted trees. In this...
Tree reconstruction from multi-state characters (2002)
Abstract. In evolutionary biology, a character is a function χ from a set X of present-day species into a finite set of states. Suppose the species in X have evolved according to a bifurcating tree...
A characterization for a set of partial partitions to define an X–tree, Discrete Mathematics (2002)
Abstract. Trees whose vertices are partially labelled by elements of a finite set X provide a natural way to represent partitions of subsets of X. The condition under which a given collection of such...
Tree reconstruction via a closure operation on partial splits (2001)
Abstract. A fundamental problem in biological classification is the reconstruction of phylogenetic trees for a set X of species from a collection of either subtrees or qualitative characters. This...
Constructing optimal trees from quartets (2001)
We present fast new algorithms for constructing phylogenetic trees from quartets Ž resolved trees on four leaves.. The problem is central to divide-and-conquer approaches to phylogenetic analysis...
Properties of phylogenetic trees generated by Yule-type speciation models (2001)
We investigate some discrete structural properties of evolutionary trees generated under simple null models of speciation, such as the Yule model. These models have been used as priors in Bayesian...
Constructing optimal trees from quartets (2001)
We present fast new algorithms for constructing phylogenetic trees from quartets (resolved trees on four leaves). The problem is central to divide and conquer approaches to phylogenetic analysis and...
Tree reconstruction via a closure operation on partial splits (2001)
Abstract. A fundamental problem in biological classification is the reconstruction of phylogenetic trees for a set X of species from a collection of either subtrees or qualitative characters. This...
A supertree method for rooted trees (2000)
Abstract. The amalgamation of leaf-labelled (phylogenetic) trees on overlapping leaf sets into one (super)tree is a central problem in several areas of classification, particularly evolutionary...
Algorithmic aspects of tree (2000)
Sebastian Böcker, Gk Strukturbildungsprozesse, Fsp Mathematisierung, David Bryant, ...
‡ Mike Steel thanks the New Zealand Marsden Fund (UOC-MIS-003) for supporting this research 1 2 BÖCKER, BRYANT, DRESS, STEEL Proposed running head: Tree amalgamation
Distributions of cherries for two models of trees (2000)
Null models for generating binary phylogenetic trees are useful for testing evolutionary hypotheses and reconstructing phylogenies. We consider two such null models ± the Yule and uniform models ±...
A supertree method for rooted trees (2000)
Abstract. The amalgamation of leaf-labelled (phylogenetic) trees on overlapping leaf sets into one (super)tree is a central problem in several areas of classi cation, particularly evolutionary...
Parsimony, Likelihood, and the Role of Models in Molecular Phylogenetics (2000)
Methods such as maximum parsimony (MP) are frequently criticized as being statistically unsound and not being based on any “model.” On the other hand, advocates of MP claim that maximum...
Invariable Sites Models and Their Use in Phylogeny Reconstruction (2000)
Steel, Mike, Huson, Daniel, Lockhart, Peter J.
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...
Modeling the covarion hypothesis of nucleotide substitution (1998)
A “covarion ” model for nucleotide substitution which allows sites to turn “on ” and “off ” with time was proposed 27 years ago by Fitch and Markowitz. It has been argued recently that...
Better Methods for Solving Parsimony and Compatibility (1998)
Maria Luisa Bonet, Mike Steel, Tandy Warnow, Shibu Yooseph
Evolutionary tree reconstruction is a challenging problem with important applications in Biology and Linguistics. In Biology, one of the most promising approaches to tree reconstruction is to find...
ELSEVIER Modeling the Covarion Hypothesis of Nucleotide Substitution (1996)
A "covarion " model for nucleotide substitution that allows sites to turn "on " and "off " with time was proposed in 1970 by Fitch and Markowitz....
The Number of Nucleotide Sites Needed to Accurately Reconstruct Large Evolutionary Trees (1996)
Mike Steel, Laszlo A. Szekely, Peter L. Erdös, P'eter L. Erdos
Biologists seek to reconstruct evolutionary trees for increasing number of species, n, from aligned genetic sequences. How fast the sequence length N must grow, as a function of n, in order to...
Expected Anomalies in the Fossil Record
The problem of intermediates in the fossil record has been frequently discussed ever since Darwin. The extent of ‘gaps’ (missing transitional stages) has been used to argue against gradual...
Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny
Gernhard, Tanja, Ford, Daniel, Vos, Rutger, Steel, Mike
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists–how can...
Hedging Our Bets: The Expected Contribution of Species to Future Phylogenetic Diversity
Steel, Mike, Mimoto, Aki, Mooers, Arne Ø.
If predictions for species extinctions hold, then the ‘tree of life’ today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species is likely...