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

/pdf/gaps-as-characters-in-sequence-based-phylogenetic-analyses-4hdlrw0k0r.pdf

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)

Acid preparation of fishes from the English Chalk allows very detailed descriptions to be prepared. The acanthopterygians of the English Chalk are redescribed, and members of all the genera known by more than one specimen are treated at length. The English Chalk genera of Ctenothrissiformes, a group confined to the Cenomanian and Lower Turonian, are also described in detail, since this group is often cited as possibly ancestral to the acanthopterygians. The acanthopterygians and Ctenothrissiformes of all other Mesozoic deposits are more briefly described. The main systematic conclusions are as follows. A new order Ctenothrissiformes is made, to replace the Bathyclupeiformes, since Bathyclupea is a percoid. Within the Ctenothrissiformes, a new family Aulolepidae is made to contain Aulolepis and Pateroperca (the latter was formerly thought to be a percoid). The order Beryciformes is divided into three new sub-orders, Polymixioidei, Dinopterygoidei and Berycoidei. The Polymixioidei contains two families, the Polymixiidae, ranging from the Cenomanian to the present, and a new monotypic family Sphenocephalidae, confined to the Upper Senonian. The family Berycopsidae is rejected, and Berycopsis is placed in the Polymixiidae. Platycormus is shown to be a synonym of Berycopsis. The Dinopterygoidei contains the Upper Senonian Dinopterygidae and three new monotypic families, the Aipichthyidae, Pharmacichthyidae and Pycnosteroididae, all of which are confined to the Cenomanian. The Berycoidei contains eleven families, all with living representatives, of which only the Trachichthyidae and Holocentridae are present in the Mesozoic. A new genus of Trachichthyidae, Tubantia, from the Upper Senonian of Westphalia, is made. The genus Hoplopteryx, previously placed in the Berycidae, is shown to be a trachichthyid, and two new species of Hoplopteryx, H. macranthus and H. gephyrognathus, both from the English Chalk, are described. Among the Perciformes, a new genus of Serranidae, Proserranus, is made for a species from the Danian of Sweden, and Bathysoma, from the same horizon and locality, is shown to be a member of the Menidae. The genus Protobrama, previously thought to be a percoid, is shown to be a member of the Tselfatiidae (Beloniformes). It is suggested that Protriacanthus, previously placed in the perciform sub-order Balistoidei, may be related to the Aulostomiformes. The main phylogenetic and stratigraphic conclusions are as follows. An analysis of the characters of acanthopterygians shows that two main trends have operated during the evolution of the group, one associated with increased manoeuvrability, and the other with changed methods of feeding. It is shown that there has been a simplification of the structure of the pars jugularis of the trigeminofacialis chamber during the evolution of the acanthopterygians from primitive teleosts. The fin spines of acanthopterygians are found to be modified lepidotrichia, not fulcral scales, but an asymmetrical structure at the base of the first ray in both the pectoral and pelvic fins of the most primitive teleosts and in the pelvic fins of several generalized groups is possibly a fulcral scale. Acanthopterygians first appear at the base of the Cenomanian. After a radiation of the Beryciformes at or before the base of the Cenomanian the acanthopterygians remained almost constant in number throughout the Cenomanian, Turonian and Senonian. Not until the Perciformes appeared did they begin to radiate into the great range of forms found today. All the acanthopterygians of the Cenomanian, Turonian and Senonian are members of the Beryciformes, and all three sub-orders of Beryciformes are already present at the base of the Cenomanian. It is suggested that the Beryciformes may be at least a diphyletic group, with the Berycoidei having an origin independent of the other two sub-orders. It is concluded that the Beryciformes arose from near the Ctenothrissiformes, but from none of the known members of this group. The two Mesozoic families of Berycoidei, the Trachichthyidae and Holocentridae, show signs of convergence towards a common type as they are traced back to the base of the Cenomanian. The Trachichthyidae appear to be ancestral to all the families of Berycoidei except the Holocentridae. Within the Cretaceous Polymixiidae there are two diverging lines, one leading to the living Polymixia and the other leading to Berycopsis, which shows marked similarities to the perciform families Scorpidae, Monodactylidae and Kyphosidae. The other family of Polymixiodei, the Sphenocephalidae, is the only known group which could be ancestral to the Serranidae, the most generalized family of Perciformes. Each of the four families of Dinopterygoidei shows resemblances to a different group of Perciformes. The Dinopterygidae, so far as they are known, resemble the Centrarchidae, the Pycnosteroididae resemble the Chaetodontidae, the Aipichthyidae show marked similarities to the Carangidae, and the Pharmacichthyidae resemble the Acanthuroidei and Balistoidei. The Perciformes appear only in the uppermost Cretaceous, where two genera are known in the Danian and one in the Montian. Six different families of Cretaceous Beryciformes show similarities to different groups of Perciformes. It is found that there is no good evidence for regarding all these similarities as due to convergence, but that some of them, and in particular those between the Aipichthyidae and Carangidae and between Berycopsis and the Scorpidae, indicate relationship. It is therefore suggested that the Perciformes is a polyphylectic group, in which several lines arose independently at a beryciform level.

A Review of Mesozoic Acanthopterygian Fishes, with Special Reference to Those of the English Chalk

An overview of the early fossil record of acanthomorphs

Synopsis A new fish fauna is described from the middle Cenomanian of Namoura, Lebanon. Thirty species are described of which 13 are new. Six new genera are erected to contain seven of these new species. These new taxa include the teleosts Ctenodentelops striatus gen. et sp. nov. (Elopidae), Lebonichthys namourensis sp. nov. (Albulidae), Triplomystus noorae gen. et sp. nov. and Triplomys‐tus oligoscutatus gen. et sp. nov. (Paraclupeidae), Armigatus namourensis sp. nov. and Armigatus alticorpus sp. nov. (Clupeomorpha incertae sedis), Scombroclupea diminuta sp. nov. (Clupeiformes incertae sedis), Enchodus mecoanalis sp. nov. (Enchodontidae), Serrilepis prymnostrigos gen. et sp. nov. and Serrilepis minor gen. et sp. nov. (Halecidae), Paracentrus lebanonensis gen. et sp. nov. (Holocentroidea) and Gigapteryx lebanonensis gen. et sp. nov. (Euacanthopterygii incertae sedis). Two new species of the aspidorhynchid genus Belonostomus are recognised but left un‐named awaiting better material, as is one newspecies of ...

Fossil fishes from the Cenomanian (Upper Cretaceous) of Namoura, Lebanon

I have been given a title concerning what Medawar (1967:23, 74) called ‘a comparatively humble and unexacting kind of science,’ research in ‘the parish registers of evolution.’ To avoid too much parochial detail, I will deal only with the phylogeny of the teleosts as a whole, without going into the different subgroups in any detail, and I shall emphasize generalities, using the teleosts as an example in a discussion of the role of phylogenetic paleontology. I shall try to assess paleontological methods, as practiced by workers on fossil teleosts, with the aim of identifying failures and successes, and of suggesting what contributions to phylogeny can and cannot be expected from paleontologists and their material. With these aims, my approach must be historical, and the main body of the paper is a historical review, with commentary. Since the teleosts are the first group for which a recognizable phylogenetic diagram was proposed (Agassiz, 1844), this review covers a longer period than most reviews of phylogenetic ideas. The review of nineteenth century work is fairly complete, but in the twentieth century, where the literature is more voluminous and well-known, I have cited only selected papers, particularly those containing phylogenetic diagrams, which summarize ideas more concisely than extended quotation.

Colin Patterson

Papers

A Review of Mesozoic Acanthopterygian Fishes, with Special Reference to Those of the English Chalk

An overview of the early fossil record of acanthomorphs

Fossil fishes from the Cenomanian (Upper Cretaceous) of Namoura, Lebanon

The Contribution of Paleontology to Teleostean Phylogeny

Lungfishes, Tetrapods, Paleontology, and Plesiomorphy