Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.

Ribosomal DNA: molecular evolution and phylogenetic inference.

In the analysis of sequence-based data matrices, the use of different methods of treating gaps has been demonstrated to in? fluence the resulting phylogenetic hypothe? ses (e.g., Eernisse and Kluge, 1993; Vogler and DeSalle, 1994; Simons and Mayden, 1997). Despite this influence, a well-justi? fied, uniformly applied method of treating gaps is lacking in sequence-based phyloge? netic studies. Treatment of gaps varies widely from secondarily mapping gaps onto the tree inferred from base characters

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Gaps as Characters in Sequence-Based Phylogenetic Analyses

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNAValine genes, ≈ 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (≈ 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The...

https://bioone.org/journals/Bulletin-of-the-American-Museum-of-Natural-History/volume-2006/issue-297/0003-0090(2006)297[0001:TATOL]2.0.CO;2/THE-AMPHIBIAN-TREE-OF-LIFE/10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2.pdf

The amphibian tree of life

-Character congruence, the principle of using all the relevant data, and character independence are important concepts in phylogenetic inference, because they relate directly to the evidence on which hypotheses are based. Taxonomic congruence, which is agreement among patterns of taxonomic relationships, is less important, because its connection to the underlying character evidence is indirect and often imperfect. Also, taxonomic congruence is difficult to justify, because of the arbitrariness involved in choosing a consensus method and index with which to estimate agreement. High levels of character congruence were observed among 89 biochemical and morphological synapomorphies scored on 10 species of Epicrates. Such agreement is consistent with the phylogenetic interpretation attached to the resulting hypothesis, which is a consensus of two equally parsimonious cladograms: (cenchria (angulifer (striatus ((chrysogaster, exsul) (inornatus, subflavus) (gracilis (fordii, monensis)))))). Relatively little (11.4%) of the character incongruence was due to the disparity between the biochemical and morphological data sets. Each of the clades in the consensus cladogram was confirmed by two or more unique and unreversed novelties, and six of the eight clades were corroborated by biochemical and morphological evidence. Such combinations of characters add confidence to the phylogenetic hypothesis, assuming the qualitatively different kinds of data are more likely to count as independent than are observations drawn from the same character system. Most of the incongruence occurred in the skeletal subset of characters, and much of that independent evolution seemed to be the result of paedomorphosis. [Biochemical data; character congruence; character independence; Epicrates; evidence; morphological data; paedomorphosis; phylogenetic systematics; taxonomic congruence; total evidence.] The goals of cladistics and phenetics are different. The former estimates phylogeny (Hennig, 1966), the latter seeks stability and convenience in classification (Sokal, 1986:424). Unfortunately, these objectives have become confused, especially where stability is concerned. For example, Hillis (1987:35) stated that "[c]lassifications are best based on information in common among multiple data sets (i.e., consensus trees), whereas the best estimate of phylogeny and best estimate of character evolution are represented in the analysis of the combined data sets." The importance of a conservative information storage-retrieval system is undeniable (e.g., International Code of Zoological Nomenclature, 1985:3), and pheneticists sought justification for their methods in this simple truth (Sokal and Sneath, 1963). Even cladists attributed some significance to stability per se, because the lack of it confounds attempts to discover the single historical pattern (Schuh and Farris, 1981). Not unexpectedly, cladists responded (e.g., Farris, 1971) to the proposition that phenetic methods produce more stable classifications (e.g., Sokal and Sneath, 1963: 264). Analytical precision was demanded by the contestants, and an incredible array of consensus methods and indexes were developed (see lists below). It is important to bear in mind that only information on taxonomic grouping can be used to evaluate the pheneticists' claims, because character congruence is difficult to judge in phenetic analyses. Eventually, the controversy over stability became a relative issue, with cladists arguing greater stability for classifications produced by their methods, as if stability was a goal of phylogenetic systematics. Further, Nelson and Platnick (1981:219; see also Nelson, 1979) attempted to justify cla-

A Concern for Evidence and a Phylogenetic Hypothesis of Relationships among Epicrates (Boidae, Serpentes)

Vertebrate Structure and History: Foreword

Vertebrate Morphology: Basic Structure and Evolution of Vertebrates. Erik Jarvik. Academic Press, New York, 1980. In two volumes. Vol. 1, xvi, 576 pp., illus. $94.50. Vol. 2, xiv, 338 pp., illus. $56.50.

Functional Morphology and Classification of Teleostean Fishes. William A. Gosline. University of Hawaii Press, Honolulu, 1971. x, 208 pp., illus. Paper, $5

Biogeography: in search of principles

Evolution: The History of an Idea. By Peter J. Bowler. University of California Press: 1984. Pp. 412. Hbk $34.45, £23.95; pbk $12.60, £8.75.

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Colin Patterson

Papers

Vertebrate Structure and History: Foreword

Vertebrate Morphology: Basic Structure and Evolution of Vertebrates. Erik Jarvik. Academic Press, New York, 1980. In two volumes. Vol. 1, xvi, 576 pp., illus. $94.50. Vol. 2, xiv, 338 pp., illus. $56.50.

Functional Morphology and Classification of Teleostean Fishes. William A. Gosline. University of Hawaii Press, Honolulu, 1971. x, 208 pp., illus. Paper, $5

Biogeography: in search of principles

Preformation to punctuation