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

https://www.cs.princeton.edu/~schapire/papers/ecolmod.pdf

Maximum entropy modeling of species geographic distributions

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

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk

/pdf/bayesian-phylogenetics-with-beauti-and-the-beast-1-7-2xkb29qdvu.pdf

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

Ecological changes in the phenology and distribution of plants and animals are occurring in all well-studied marine, freshwater, and terrestrial groups These observed changes are heavily biased in the directions predicted from global warming and have been linked to local or regional climate change through correlations between climate and biological variation, field and laboratory experiments, and physiological research Range-restricted species, particularly polar and mountaintop species, show severe range contractions and have been the first groups in which entire species have gone extinct due to recent climate change Tropical coral reefs and amphibians have been most negatively affected Predator-prey and plant-insect interactions have been disrupted when interacting species have responded differently to warming Evolutionary adaptations to warmer conditions have occurred in the interiors of species’ ranges, and resource use and dispersal have evolved rapidly at expanding range margins Observed genetic shifts modulate local effects of climate change, but there is little evidence that they will mitigate negative effects at the species level

https://www.fws.gov/southwest/es/documents/R2ES/LitCited/LPC_2012/Parmesan_2006.pdf

Ecological and Evolutionary Responses to Recent Climate Change

Diverse historical and ecological factors determine and drive diversification of vertebrate lineages. Historical factors (e.g., orogenic movements) are expected to act on coarser spatial and temporal scales than contemporary ecological factors (e.g., climate and biotic interactions). However, distinctions between such scales remain arbitrary, and yet are important to understanding which factors acted in the emergence of new species. We inferred ancestral states for climatic niches on ecological scales, and ancestral area reconstructions for the genus Geositta on deeper time scales. Ecological niches did not overlap more between sister species than among more distant relatives, and rather pointed to a plastic scenario for climatic diversification of Geositta rather than niche conservatism. Events temporally associated with the formation of the Andes (Miocene) seem to explain most of the diversification. In sum, climatic factors may not have had a great influence in the diversification of Geositta, at least in the context of Pleistocene climate fluctuations.

Ecological and historical views of the diversification of Geositta miners (Aves: Furnariidae: Sclerurinae)

Climate change biology is seeing a wave of new contributions, which are reviewed herein. Contributions treat shifts in phenology and distribution, and both document past and forecast future effects. However, many of the current wave of contributions are observational and correlational, and few are experimental in nature, and too often a conceptual framework in which to contextualize the results is lacking. An additional gap is the lack of effective cross-linking among areas of research, for example, connection of sea-level rise and climate change implications for distributions of species, or evolutionary adaptation studies with distributional shift studies. Although numerous important contributions have emerged in recent years, synthesis of this phenomenon and its consequences has not yet been achieved.  2010 John Wiley & Sons, Ltd. WIREs Clim Change

/pdf/recent-advances-in-the-climate-change-biology-literature-4hu8lkj63w.pdf

Recent advances in the climate change biology literature: describing the whole elephant

. Henslow's Sparrows (Ammodramus henslowii) are distributed in tallgrass prairies in central North America; however, this species is restricted further to specific habitats within these prairies—large expanses with relatively little woody vegetation but an accumulation of standing grasses and forbs, conditions that result from infrequent disturbances by fire, mowing, or grazing. Henslow's Sparrows have been documented to be unpredictable at breeding sites from year to year, but studies to date have considered only local spatial scales. We compared resettlement behavior (prevalence of occurrence and variation in abundance) of Henslow's Sparrows to that of two other grassland sparrows, Grasshopper Sparrows (A. savannarum) and Savannah Sparrows (Passerculus sandwichensis), across multiple spatial resolutions. In Henslow's Sparrows, prevalence was lower and variation in abundance was greater than in the other two species. Indeed, Henslow's Sparrows do not occur consistently at extents of less than 120...

/pdf/spatial-scaling-of-prevalence-and-population-variation-in-1hyr0yfsx0.pdf

Spatial Scaling of Prevalence and Population Variation in Three Grassland Sparrows

Parsimony analysis of endemism (PAE) has become a popular analytical approach in efforts to map the biogeography of Mexican biotas. Although attractive, the technique has serious drawbacks that make correct inferences of biogeographic history unlikely, which has been noted amply in the broader literature.

/pdf/parsimony-analysis-of-endemism-pae-and-studies-of-mexican-11rfqo0ssw.pdf

Parsimony analysis of endemism (PAE) and studies of Mexican biogeography PAE y el estudio de la biogeografía de México

A new highland species of chestnut-capped Arremon brush-finch is described from the Sierra Madre del Sur of central Guerrero. This form, although indistinguishable in external phenotype from adjacent populations to the east in Oaxaca, is dramatically differentiated in mitochondrial DNA sequence characters, and quite unexpectedly is the sister lineage to the very distinct (phenotype and genotype), central-Mexican-endemic A. virenticeps. Nuclear sequence differentiation in the new lineage is more subtle than in mitochondrial DNA, but is on par with that in the well-marked A. virenticeps. The new species is thus distinct from its sister lineage in genotype and phenotype, and clearly distinct from all other forms in genotype; however, it has retained an ancestral external phenotype similar to other members of the broader A. brunneinucha complex.

https://bioone.org/journals/The-Wilson-Journal-of-Ornithology/volume-125/issue-3/12-136.1/A-new-species-of-Brush-Finch-span-classgenus-speciesArremon-span/10.1676/12-136.1.pdf

A. Townsend Peterson

Papers

Ecological and historical views of the diversification of Geositta miners (Aves: Furnariidae: Sclerurinae)

Recent advances in the climate change biology literature: describing the whole elephant

Spatial Scaling of Prevalence and Population Variation in Three Grassland Sparrows

Parsimony analysis of endemism (PAE) and studies of Mexican biogeography PAE y el estudio de la biogeografía de México

A new species of Brush-Finch (Arremon; Emberizidae) from western Mexico