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Maps Between Trees and Cladistic Analysis of Historical Associations among Genes,Organisms, and Areas

https://doi.org/10.1093/sysbio/43.1.58

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-642-84622-9openalex-snapshot

Molecular Evolution of the Major Histocompatibility Complex

inferredcites →https://doi.org/10.1007/bf01894195openalex-snapshot

Consensus supertrees: The synthesis of rooted trees containing overlapping sets of labeled leaves

inferredcites →https://doi.org/10.1038/332258a0openalex-snapshot

Phylogenetic trees support the coevolution of parasites and their hosts

inferredcites →https://doi.org/10.1038/351619a0openalex-snapshot

Comparative methods for explaining adaptations

inferredcites →https://doi.org/10.1093/genetics/122.4.957openalex-snapshot

Gene genealogy in three related populations: consistency probability between gene and population trees.

inferredcites →https://doi.org/10.1093/genetics/127.2.429openalex-snapshot

Inferences of species phylogeny in relation to segregation of ancient polymorphisms.

inferredcites →https://doi.org/10.1093/sysbio/28.1.1openalex-snapshot

Cladistic Analysis and Synthesis: Principles and Definitions, with a Historical Note on Adanson's Familles Des Plantes (1763-1764)

inferredcites →https://doi.org/10.1093/sysbio/28.2.132openalex-snapshot

Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences

inferredcites →https://doi.org/10.1093/sysbio/37.3.254openalex-snapshot

Quantitative Cladistic Biogeography: Constructing and Comparing Area Cladograms

inferredcites →https://doi.org/10.1093/sysbio/37.4.315openalex-snapshot

Parsimony in Vicariance Biogeography: A Quantitative Method and a Greater Antillean Example

inferredcites →https://doi.org/10.1093/sysbio/40.2.188openalex-snapshot

Clocks, Clades, and Cospeciation: Comparing Rates of Evolution and Timing of Cospeciation Events in Host-Parasite Assemblages

inferredcites →https://doi.org/10.1093/sysbio/40.4.470openalex-snapshot

Three-Area Statements: Standard Assumptions for Biogeographic Analysis

inferredcites →https://doi.org/10.1093/sysbio/42.1.77openalex-snapshot

Genes, Organisms, and Areas: The Problem of Multiple Lineages

inferredcites →https://doi.org/10.1111/j.1096-0031.1990.tb00532.xopenalex-snapshot

COMPONENT ANALYSIS: A VALIANT FAILURE?

inferredcites →https://doi.org/10.2307/1222480openalex-snapshot

Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees

inferredcites →https://doi.org/10.2307/2412448openalex-snapshot

Distinguishing Homologous from Analogous Proteins

inferredcites →https://doi.org/10.2307/2412808openalex-snapshot

A Method of Analysis for Historical Biogeography

inferredcites →https://doi.org/10.2307/2412970openalex-snapshot

Vicariant Patterns and Historical Explanation in Biogeography

inferredcites →https://doi.org/10.2307/2419070openalex-snapshot

Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy

inferredcites →https://doi.org/10.2307/2992181openalex-snapshot

Cospeciation in Host-Parasite Assemblages: Comparative Analysis of Rates of Evolution and Timing of Cospeciation Events

inferredcites →https://doi.org/10.2307/2992182openalex-snapshot

Temporal Congruence and Cladistic Analysis of Biogeogrphy and Cospeciation

inferredcites →https://doi.org/10.2307/2992205openalex-snapshot

Parsimony Analysis in Historical Biogeography and Coevolution: Methodological and Theoretical Update

inferredcites →https://doi.org/10.5860/choice.39-2183openalex-snapshot

MacClade 4.0: analysis of phylogeny and character evolution

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Nematode endoparasites do not codiversify with their stick insect hosts

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A Different Tempo of Mitochondrial DNA Evolution in Birds and Their Parasitic Lice

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Reconstructing Domain Compositions of Ancestral Multi-domain Proteins

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New Efficient Algorithm for Modeling Partial and Complete Gene Transfer Scenarios

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Gene Trees and Species Trees: The Gene-Duplication Problem is Fixed-Parameter Tractable

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The asymmetric median tree — A new model for building consensus trees

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Analogs and Duals of the MAST Problem for Sequences and Trees

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Evolution Of Actinorhizal Host Plants And Frankia Endosymbionts

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Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

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Gene Phylogenies and Orthologous Groups

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Analysis of Gene Order Evolution Beyond Single-Copy Genes

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A Linear-Time Algorithm for Reconciliation of Non-binary Gene Tree and Binary Species Tree

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Fast Algorithms for Inferring Gene-Species Associations

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Mean Values of Gene Duplication and Loss Cost Functions

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Bootstrapping Algorithms for Gene Duplication and Speciation Events

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Coestimation of Gene Trees and Reconciliations Under a Duplication-Loss-Coalescence Model

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New Algorithms for the Genomic Duplication Problem

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New Efficient Algorithm for Detection of Horizontal Gene Transfer Events

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Consensus tree method for generating master assembly sequence

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Mathematical properties of the gene duplication cost

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Gene tree correction for reconciliation and species tree inference: Complexity and algorithms

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Knowledge-based model for constructing master assembly sequence

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A scalable parallelization of the gene duplication problem

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Fast algorithm for the reconciliation of gene trees and LGT networks

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Reconciliation of a gene network and species tree

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Analytical methods in palaeobiogeography, and the role of early vertebrate studies

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DLS-trees: A model of evolutionary scenarios

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New Approaches for Inferring Phylogenies in the Presence of Paralogs

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Historical biogeography, ecology and species richness

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Comparative population genetics and phylogeography of two lacertid lizards (Eremias argus and E. brenchleyi) from China

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Phylogenetic and cophylogenetic relationships of entomopathogenic nematodes (Heterorhabditis: Rhabditida) and their symbiotic bacteria (Photorhabdus: Enterobacteriaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2017.03.003openalex-snapshot

Cophylogenetics and biogeography reveal a coevolved relationship between sloths and their symbiont algae

inferred← citeshttps://doi.org/10.1016/j.ympev.2018.09.003openalex-snapshot

Molecular phylogenetics of Aspidiotini armored scale insects (Hemiptera: Diaspididae) reveals rampant paraphyly, curious species radiations, and multiple origins of association with Melissotarsus ants (Hymenoptera: Formicidae)

inferred← citeshttps://doi.org/10.1016/s0020-7519(01)00199-0openalex-snapshot

Analytical approaches to measuring cospeciation of host and parasites: through a glass, darkly

inferred← citeshttps://doi.org/10.1016/s0020-7519(01)00200-4openalex-snapshot

Co-evolutionary relationships between the nematode subfamily Cloacininae and its macropodid marsupial hosts

inferred← citeshttps://doi.org/10.1016/s0020-7519(98)00136-2openalex-snapshot

Plastids are widespread and ancient in parasites of the phylum Apicomplexafn1fn1Note: Nucleotide sequence data reported in this paper are available in the embl, GenBankTM and DDJB databases under the accession numbers AF040968–76 and AF041437–8.

inferred← citeshttps://doi.org/10.1016/s0025-5564(97)10012-8openalex-snapshot

Jungles: a new solution to the host/parasite phylogeny reconciliation problem

inferred← citeshttps://doi.org/10.1016/s0065-2458(06)68002-9openalex-snapshot

Models and Methods in Comparative Genomics

inferred← citeshttps://doi.org/10.1016/s0076-6879(05)95036-2openalex-snapshot

Analytical Methods for Detecting Paralogy in Molecular Datasets

inferred← citeshttps://doi.org/10.1016/s0166-218x(98)00068-7openalex-snapshot

On the equivalence of two tree mapping measures

inferred← citeshttps://doi.org/10.1016/s0169-5347(01)02394-1openalex-snapshot

The human zoo: endogenous retroviruses in the human genome

inferred← citeshttps://doi.org/10.1016/s0169-5347(97)01242-1openalex-snapshot

Phylogenetic supertrees: Assembling the trees of life

inferred← citeshttps://doi.org/10.1016/s0169-5347(98)01438-4openalex-snapshot

Trees within trees: phylogeny and historical associations

inferred← citeshttps://doi.org/10.1016/s0196-6774(03)00081-6openalex-snapshot

Analogs & duals of the MAST problem for sequences & trees

inferred← citeshttps://doi.org/10.1016/s0748-3007(02)00007-5openalex-snapshot

Testing the accuracy of TreeMap and Brooks parsimony analyses of coevolutionary patterns using artificial associations

inferred← citeshttps://doi.org/10.1016/s0748-3007(03)00048-3openalex-snapshot

A priori and a posteriori methods in comparative evolutionary studies of host–parasite associations

inferred← citeshttps://doi.org/10.1016/s1055-7903(02)00033-7openalex-snapshot

Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes

inferred← citeshttps://doi.org/10.1016/s1055-7903(03)00109-xopenalex-snapshot

Gene tree parsimony vs. uninode coding for phylogenetic reconstruction

inferred← citeshttps://doi.org/10.1016/s1567-1348(01)00003-xopenalex-snapshot

Evolution of the Old World Arenaviridae and their rodent hosts: generalized host-transfer or association by descent?

inferred← citeshttps://doi.org/10.1017/9781139047678openalex-snapshot

Cladistics

inferred← citeshttps://doi.org/10.1017/9781139047678.001openalex-snapshot

Preface

inferred← citeshttps://doi.org/10.1017/9781139047678.002openalex-snapshot

Introduction: Carving Nature at Its Joints, or Why Birds Are Not Dinosaurs and Men Are Not Apes

inferred← citeshttps://doi.org/10.1017/9781139047678.003openalex-snapshot

The Interrelationships of Organisms

inferred← citeshttps://doi.org/10.1017/9781139047678.004openalex-snapshot

What This Book Is About

inferred← citeshttps://doi.org/10.1017/9781139047678.005openalex-snapshot

Classification

inferred← citeshttps://doi.org/10.1017/9781139047678.006openalex-snapshot

Systematics: Exposing Myths

inferred← citeshttps://doi.org/10.1017/9781139047678.007openalex-snapshot

Relationship Diagrams

inferred← citeshttps://doi.org/10.1017/9781139047678.008openalex-snapshot

Essentialism and Typology

inferred← citeshttps://doi.org/10.1017/9781139047678.009openalex-snapshot

Monothetic and Polythetic Taxa

inferred← citeshttps://doi.org/10.1017/9781139047678.010openalex-snapshot

Non-taxa or the Absence of –Phyly: Paraphyly and Aphyly

inferred← citeshttps://doi.org/10.1017/9781139047678.011openalex-snapshot

The Cladistic Programme

inferred← citeshttps://doi.org/10.1017/9781139047678.012openalex-snapshot

Parameters of Classification:Ordo Ab Chao

inferred← citeshttps://doi.org/10.1017/9781139047678.013openalex-snapshot

How to Study Classification

inferred← citeshttps://doi.org/10.1017/9781139047678.014openalex-snapshot

Modern Artificial Methods and Raw Data

inferred← citeshttps://doi.org/10.1017/9781139047678.015openalex-snapshot

How to Study Classification: Consensus Techniques and General Classifications

inferred← citeshttps://doi.org/10.1017/9781139047678.016openalex-snapshot

How to Study Classification: ‘Total Evidence’ vs. ‘Consensus’, Character Congruence vs. Taxonomic Congruence, Simultaneous Analysis vs. Partitioned Data

inferred← citeshttps://doi.org/10.1017/9781139047678.017openalex-snapshot

How to Study Classification

inferred← citeshttps://doi.org/10.1017/9781139047678.018openalex-snapshot

How to Study Classification

inferred← citeshttps://doi.org/10.1017/9781139047678.019openalex-snapshot

Beyond Classification

inferred← citeshttps://doi.org/10.1017/9781139047678.020openalex-snapshot

Beyond Classification: How to Study Phylogeny

inferred← citeshttps://doi.org/10.1017/9781139047678.021openalex-snapshot

The Separation of Classification and Phylogenetics

inferred← citeshttps://doi.org/10.1017/9781139047678.022openalex-snapshot

Further Myths and More Misunderstandings

inferred← citeshttps://doi.org/10.1017/9781139047678.023openalex-snapshot

Afterword

inferred← citeshttps://doi.org/10.1017/9781139047678.024openalex-snapshot

Index

inferred← citeshttps://doi.org/10.1017/9781139047678.025openalex-snapshot

Systematics Association Special Volumes

inferred← citeshttps://doi.org/10.1017/s0031182002001841openalex-snapshot

Revealing the faunal tapestry: co-evolution and historical biogeography of hosts and parasites in marine systems

inferred← citeshttps://doi.org/10.1017/s0031182002002792openalex-snapshot

The phylogeny of the Schistosomatidae based on three genes with emphasis on the interrelationships of Schistosoma Weinland, 1858

inferred← citeshttps://doi.org/10.1017/s1464793104006463openalex-snapshot

Cophylogeny of the Ficus microcosm

inferred← citeshttps://doi.org/10.1023/a:1006255822947openalex-snapshot

Have chondracanthid copepods co-speciated with their teleost hosts?

inferred← citeshttps://doi.org/10.1038/415784aopenalex-snapshot

Chameleon radiation by oceanic dispersal

inferred← citeshttps://doi.org/10.1038/jid.2009.94openalex-snapshot

Cutaneotropic Human β-/γ-Papillomaviruses Are Rarely Shared between Family Members

inferred← citeshttps://doi.org/10.1038/npre.2007.1030.1openalex-snapshot

Treemap Versus BPA (Again): A Response to Dowling

inferred← citeshttps://doi.org/10.1046/j.0305-0270.2003.00982.xopenalex-snapshot

Dispersal vs. vicariance in the Mediterranean: historical biogeography of the Palearctic Pachydeminae (Coleoptera, Scarabaeoidea)

inferred← citeshttps://doi.org/10.1046/j.1365-2699.1996.00968.xopenalex-snapshot

Biogeography of the phoracanthine beetles (Coleoptera: Cerambycidae)

inferred← citeshttps://doi.org/10.1046/j.1365-2699.2001.00519.xopenalex-snapshot

When simplicity is not parsimonious: a priori and a posteriori methods in historical biogeography

inferred← citeshttps://doi.org/10.1046/j.1365-2699.2001.00523.xopenalex-snapshot

The voice of historical biogeography

inferred← citeshttps://doi.org/10.1046/j.1365-2699.2003.00848.xopenalex-snapshot

Critique of parsimony analysis of endemicity as a method of historical biogeography

inferred← citeshttps://doi.org/10.1046/j.1365-2699.2003.00928.xopenalex-snapshot

Phylogenetic biogeography deconstructed

inferred← citeshttps://doi.org/10.1046/j.1365-294x.1998.00317.xopenalex-snapshot

Comparative phylogeography and the identification of genetically divergent areas for conservation

inferred← citeshttps://doi.org/10.1046/j.1365-294x.1998.00334.xopenalex-snapshot

Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia

inferred← citeshttps://doi.org/10.1046/j.1365-294x.2000.01032.xopenalex-snapshot

Comparative avian phylogeography of Cameroon and Equatorial Guinea mountains: implications for conservation

inferred← citeshttps://doi.org/10.1046/j.1365-294x.2001.01220.xopenalex-snapshot

The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a medically important snake, Trimeresurus albolabris

inferred← citeshttps://doi.org/10.1046/j.1365-294x.2003.01721.xopenalex-snapshot

Associations between mycophagous Drosophila and their Howardula nematode parasites: a worldwide phylogenetic shuffle

inferred← citeshttps://doi.org/10.1046/j.1365-294x.2003.01794.xopenalex-snapshot

Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province

inferred← citeshttps://doi.org/10.1046/j.1463-6409.2003.00130.xopenalex-snapshot

Context of diversification of the viviparous Gyrodactylidae (Platyhelminthes, Monogenoidea)

inferred← citeshttps://doi.org/10.1071/bt00027openalex-snapshot

Most parsimonious areagrams versus fossils: the case of Nothofagus (Nothofagaceae)

inferred← citeshttps://doi.org/10.1071/bt11053openalex-snapshot

Codiversification of orchids (Pterostylidinae) and their associated mycorrhizal fungi

inferred← citeshttps://doi.org/10.1071/is12010openalex-snapshot

Biogeography of the Cantacaderinae Stål (Insecta : Heteroptera : Tingidae) revisited

inferred← citeshttps://doi.org/10.1071/sb24011openalex-snapshot

Navigating phylogenetic conflict and evolutionary inference in plants with target-capture data

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