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

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

▪ Abstract Many uses of gene trees implicitly assume that nominal species are monophyletic in their alleles at the study locus. However, in well-sampled gene trees, certain alleles in one species may appear more closely related to alleles from different species than to other conspecific alleles. Such deviations from species-level monophyly have a variety of causes and may lead to erroneous evolutionary interpretations if undetected. The present paper describes the causes and consequences of these paraphyletic and polyphyletic patterns. It also provides a detailed literature survey of mitochondrial DNA studies on low-level animal phylogeny and phylogeography, results from which reveal the frequency of nonmonophyly and patterns of interpretation and sampling. This survey detected species-level paraphyly or polyphyly in 23% of 2319 assayed species, demonstrating this phenomenon to be statistically supported, taxonomically widespread, and far more common than generally recognized. Our findings call for increa...

Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA

The origins and development of the study of speciation, hybrid zones and phylogeography are outlined using evolutionary iconography. This traces the ideas in this field from Lamarck and Darwin through to the present as represented in diagrams and figures. A ‘tree of trees’ summarizes this growth and current vitality. The new facility to use various DNA sequences from nuclear, mitochondrial and chloroplast genomes to determine genetic variation throughout a species range is examined particularly. There is great genomic subdivision across species distributions, which can be interpreted in the light of the recent demonstrations of severe palaeoclimatic oscillations. Refugia and postglacial colonization routes are proposed for several organisms across Europe. The role of geography in speciation through the Pleistocene is considered. These emerging principles and analyses are applied to data available on a variety of organisms in other regions of the world, such as the Arctic, North America and the Tropics, and including the progress of Homo sapiens through the last ice age. Some suggestions are made for future research directions.

http://webpages.icav.up.pt/PTDC/BIA-BEC/104097/2008/7.pdf

Speciation, hybrid zones and phylogeography - or seeing genes in space and time.

Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.

/pdf/bayes-or-bootstrap-a-simulation-study-comparing-the-4afd38srqj.pdf

Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence

http://www.csun.edu/~dgray/BE528/LealRodriguezRoblesAnoles.pdf

Signalling displays during predator-prey interactions in a Puerto Rican anole, Anolis cristatellus

Molecular Systematics of New World Gopher, Bull, and Pinesnakes (Pituophis: Colubridae), a Transcontinental Species Complex

Effects of display size, flowering phenology, and nectar availability on effective visitation frequency in comparettia falcata (orchidaceae)

Studies of food relations are important to our understanding of ecology at the individual, population and community levels. Detailed documentation of the diet of large-bodied, widespread snakes allows us to assess size-dependent and geographical variation in feeding preferences of gape-limited predators. Furthermore, with knowledge of the food habits of sympatric taxa we can explore possible causes of interspecific differences in trophic niches. The feeding ecology of the North American gopher snake, Pituophis catenifer, was studied based on the stomach contents of more than 2600 preserved and free-ranging specimens, and published and unpublished dietary records. Of 1066 items, mammals (797, 74.8%), birds (86, 8.1%), bird eggs (127, 11.9%), and lizards (35, 3.3%) were the most frequently eaten prey. Gopher snakes fed upon subterranean, nocturnal and diurnal prey. The serpents are primarily diurnal, but can also be active at night. Therefore, gopher snakes captured their victims by actively searching underground tunnel systems, retreat places and perching sites during the day, or by pursuing them or seizing them while they rested at night. Gopher snakes of all sizes preyed on mammals, but only individuals larger than 40 and 42 cm in snout–vent length took bird eggs and birds, respectively, possibly due to gape constraints in smaller serpents. Specimens that ate lizards were smaller than those that consumed mammals or birds. Gopher snakes raided nests regularly, as evidenced by the high frequency of nestling mammals and birds and avian eggs eaten. Most (332) P. catenifer contained single prey, but 95 animals contained 2–35 items. Of the 321 items for which direction of ingestion was determined, 284 (88.5%) were swallowed head-first, 35 (10.9%) were ingested tail-first, and two (0.6%) were taken sideways. Heavier gopher snakes took heavier prey, but heavier serpents ingested prey with smaller mass relative to snake mass, evidence that the lower limit of prey mass did not increase with snake mass. Specimens from the California Province and Arid Deserts (i.e. Mojave, Sonoran and Chihuahuan Deserts) took the largest proportion of lizards, whereas individuals from the Great Basin Desert consumed a higher percentage of mammals than serpents from other areas, and P. catenifer from the Great Plains ate a greater proportion of bird eggs. Differences in prey availability among biogeographical regions and unusual circumstances of particular gopher snake populations may account for these patterns. Gopher snakes have proportionally longer heads than broadly sympatric Rhinocheilus lecontei (long-nosed snake), Charina bottae (rubber boa) and Lampropeltis zonata (California mountain kingsnake), which perhaps explains why, contrary to the case in P. catenifer, the smaller size classes of those three species do not eat mammals. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 77, 165–183.

Feeding ecology of North American gopher snakes (Pituophis catenifer, Colubridae)

The phylogeography of the California mountain kingsnake, Lampropeltis zonata , was studied using mitochondrial DNA sequences from specimens belonging to the seven recognized subspecies and collected throughout the range of the species. Maximum parsimony and maximum likelihood methods identified a basal split within L. zonata that corresponds to southern and northern segments of its distribution. The southern clade is composed of populations from southern California (USA) and northern Baja California, Mexico. The northern clade is divided into two subclades, a ‘coastal’ subclade, consisting of populations from the central coast of California and the southern Sierra Nevada Mountains of eastern California, and a ‘northeastern’ subclade, mainly comprised of populations north of the San Francisco Bay and from the majority of the Sierra Nevada. We suggest that past inland seaways in southwestern California and the embayment of central California constituted barriers to gene flow that resulted in the two deepest divergences within L. zonata . Throughout its evolutionary history, the northern clade apparently has undergone instances of range contraction, isolation, differentiation, and then expansion and secondary contact. Examination of colour pattern variation in 321 living and preserved specimens indicated that the two main colour pattern characters used to define the subspecies of L. zonata are so variable that they cannot be reliably used to differentiate taxonomic units within this complex, which calls into question the recognition of seven geographical races of this snake.

Javier A. Rodríguez-Robles

Papers

Signalling displays during predator-prey interactions in a Puerto Rican anole, Anolis cristatellus

Molecular Systematics of New World Gopher, Bull, and Pinesnakes (Pituophis: Colubridae), a Transcontinental Species Complex

Effects of display size, flowering phenology, and nectar availability on effective visitation frequency in comparettia falcata (orchidaceae)

Feeding ecology of North American gopher snakes (Pituophis catenifer, Colubridae)

Phylogeography of the California mountain kingsnake, Lampropeltis zonata (Colubridae)