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

Without epithelial–mesenchymal transitions, in which polarized epithelial cells are converted into motile cells, multicellular organisms would be incapable of getting past the blastula stage of embryonic development. However, this important developmental programme has a more sinister role in tumour progression. Epithelial–mesenchymal transition provides a new basis for understanding the progression of carcinoma towards dedifferentiated and more malignant states.

Epithelial–mesenchymal transitions in tumour progression

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Modern Applied Statistics With S

Summary
We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees.
ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree.
The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion.
A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images.
The package ggtree is released under the artistic-2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).

https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.12628

ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

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

Miniaturization, or the evolution of extremely small adult body size, is a widespread phenomenon in animals. It has important consequences for both organismal biology and phyletic diversification above the species level. The miniaturized phenotype is a complex combination of ancestral and derived traits, including reduction and structural simplification, increased variability, and morphological novelty. Many features likely represent secondary consequences of size decrease, which may be the result of selection primarily for small body size or some related attribute such as life history characteristics. In some cases, miniaturization has resulted in novel bauplans associated with the origin of higher taxa. Evaluation of causes and consequences of miniaturization should consider obvious feattires of physical size as well as less obvious, but biologically important, features such as genome and cell size.

https://www.jstor.org/stable/pdfplus/2097188.pdf

Miniaturization of Body Size: Organismal Consequences and Evolutionary Significance

&p.1: Embryos of different species of vertebrate share a common organisation and often look similar. Adult differences among species become more apparent through divergence at later stages. Some authors have suggested that members of most or all vertebrate clades pass through a virtually identical, conserved stage. This idea was promoted by Haeckel, and has recently been revived in the context of claims regarding the universality of developmental mechanisms. Thus embryonic resemblance at the tailbud stage has been linked with a conserved pattern of developmental gene expression ‐ the zootype. Haeckel’s drawings of the external morphology of various vertebrates remain the most comprehensive comparative data purporting to show a conserved stage. However, their accuracy has been questioned and only a narrow range of species was illustrated. In view of the current widespread interest in evolutionary developmental biology, and especially in the conservation of developmental mechanisms, re-examination of the extent of variation in vertebrate embryos is long overdue. We present here the first review of the external morphology of tailbud embryos, illustrated with original specimens from a wide range of vertebrate groups. We find that embryos at the tailbud stage ‐ thought to correspond to a conserved stage ‐ show variations in form due to allometry, heterochrony, and differences in body plan and somite number. These variations foreshadow important differences in adult body form. Contrary to recent claims that all vertebrate embryos pass through a stage when they are the same size, we find a greater than 10-fold variation in greatest length at the tailbud stage. Our survey seriously undermines the credibility of Haeckel’s drawings, which depict not a conserved stage for vertebrates, but a stylised amniote embryo. In fact, the taxonomic level of greatest resemblance among vertebrate embryos is below the subphylum. The wide variation in morphology among vertebrate embryos is difficult to reconcile with the idea of a phyogenetically-conserved tailbud stage, and suggests that at least some developmental mechanisms are not highly constrained by the zootype. Our study also highlights the dangers of drawing general conclusions about vertebrate development from studies of gene expression in a small number of laboratory species. &kwd:words Morphogenesis · Developmental biology · Comparative anatomy · Comparative study · Embryology&bdy:

There is no highly conserved embryonic stage in the vertebrates : implications for current theories of evolution and development

Publisher Summary This chapter discusses whole-mount staining of xenopus and other vertebrates. Whole-mount staining makes the analysis of normal and experimentally manipulated embryos much simpler. It can be used in the assay of cellular differentiation in induction and tissue recombination experiments. It should be possible not only to assay for the indication of specific tissues, but to characterize the three-dimensional relationships between the tissue types. Whole-mount staining greatly simplifies the characterization of the expressions patterns of exogenous DNAs. Similarly, the effects of injected antibodies, antisense reagents, or the ecotopic expression of specific molecules on development can be analyzed rapidly. The prerequisite for any whole-mount analysis is that one is able to see through the specimen. This means either that the specimen must be naturally transparent, a rare feature among higher metazoans, or that it must be possible to “clear” it. Clearing generally involves two steps: extracting material from the specimen, then matching the refractive index of the bulk of the specimen remaining, thereby rendering it transparent. Primary considerations in selecting a clearing agent are how closely it matches the refractive index of the specimen, its inherent toxicity, and its compatibility with the staining reagents used.

Whole-mount staining of Xenopus and other vertebrates.

Sexually receptive female Spermophilus beldingi (Rodentia: Sciuridae) usually mate with several different males. The paternity of 27 litters born in 1977 and 1978 was ascertained by combining field observations of mating with laboratory paternity exclusion analyses. Most of the litters (78 percent) were multiply sired, usually by two or three males. This may be the highest frequency of multiple paternity ever directly demonstrated in a natural population.

Multiple paternity in Belding's ground squirrel litters.

Loss of limb skeletal elements is a recurring theme in tetrapod evolution, but the developmental mechanisms underlying this phenomenon remain largely unknown. The Australian lizard genus Hemiergis offers an excellent model system to study limb reduction among closely related, naturally occurring populations with different numbers of digits. Evolutionary digit loss in Hemiergis does not result from simple truncation of a pentadactyl skeletal developmental program. Rather, the duration of embryonic expression of the patterning molecule Sonic hedgehog (SHH) is shortened in limbs with reduced numbers of digits, and is correlated with decreased cell proliferation in the posterior aspect of the limb. Moreover, this comparative analysis suggests an early role for SHH in specification of digit identity and later importance in maintaining cell proliferation and survival. Subtle changes in spatial or temporal regulation of SHH may alter proliferation and patterning of the developing limb, thereby effecting divergence in adult limb morphology among closely related species. In contrast, expression of MSX and Distal-less proteins were similar among embryos from different populations. J. Exp. Zool. (Mol. Dev. Evol.) 297B:48-56, 2003. r 2003 Wiley-

James Hanken

Papers

Miniaturization of Body Size: Organismal Consequences and Evolutionary Significance

There is no highly conserved embryonic stage in the vertebrates : implications for current theories of evolution and development

Whole-mount staining of Xenopus and other vertebrates.

Multiple paternity in Belding's ground squirrel litters.

Developmental basis of evolutionary digit loss in the Australian lizard Hemiergis