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

▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community ...

/pdf/phylogenies-and-community-ecology-52euwskuu7.pdf

Phylogenies and Community Ecology

I. the origin of species by means of natural selection

To a first approximation, the distribution of biodiversity across the Earth can be described in terms of a relatively small number of broad-scale spatial patterns. Although these patterns are increasingly well documented, understanding why they exist constitutes one of the most significant intellectual challenges to ecologists and biogeographers. Theory is, however, developing rapidly, improving in its internal consistency, and more readily subjected to empirical challenge.

Global patterns in biodiversity

Aim Beta diversity (variation of the species composition of assemblages) may reflect two different phenomena, spatial species turnover and nestedness of assemblages, which result from two antithetic processes, namely species replacement and species loss, respectively. The aim of this paper is to provide a unified framework for the assessment of beta diversity, disentangling the contribution of spatial turnover and nestedness to beta-diversity patterns.

Innovation  I derive an additive partitioning of beta diversity that provides the two separate components of spatial turnover and nestedness underlying the total amount of beta diversity. I propose two families of measures of beta diversity for pairwise and multiple-site situations. Each family comprises one measure accounting for all aspects of beta diversity, which is additively decomposed into two measures accounting for the pure spatial turnover and nestedness components, respectively. Finally, I provide a case study using European longhorn beetles to exemplify the relevance of disentangling spatial turnover and nestedness patterns.

Main conclusion  Assigning the different beta-diversity patterns to their respective biological phenomena is essential for analysing the causality of the processes underlying biodiversity. Thus, the differentiation of the spatial turnover and nestedness components of beta diversity is crucial for our understanding of central biogeographic, ecological and conservation issues.

/pdf/partitioning-the-turnover-and-nestedness-components-of-beta-2tj8148btj.pdf

Partitioning the turnover and nestedness components of beta diversity

An important issue in the study of biodiversity is the extent to which global patterns of species richness reflect large-scale processes and historical contingencies1,2. Ecological interactions in local assemblages may constrain the number of species that can coexist3,4, but differences in diversity in similar habitats within different regions (diversity anomalies) suggest that this limit is not firm. Variation in rate of species production could influence regional and perhaps local diversity independently of the ecological capacity of an area to support coexisting species, thereby creating diversity anomalies5,6. Temperate Zone genera of plants that are disjunct between similar environments in eastern Asia and eastern North America (EAS-ENA) have twice as many species in Asia as in North America7. Because lineages of these genera in Asia and North America are mostly sister pairs8, they share a common history of adaptation and ecological relationship before disjunction. Thus, the diversity anomaly in EAS-ENA genera is not an artefact of taxon or habitat sampling but reflects differences in the net diversification (speciation–extinction) of the lineages in each of the continents. Here we propose that the most probable cause of the EAS-ENA anomaly in diversity is the extreme physiographical heterogeneity of temperate eastern Asia, especially compared with eastern North America, which in conjunction with climate and sea-level change has provided abundant opportunities for evolutionary radiation through allopatric speciation.

Large-scale processes and the Asian bias in species diversity of temperate plants

We present V.PhyloMaker, a freely available package for R designed to generate phylogenies for vascular plants. The mega‐tree implemented in V.PhyloMaker (i.e. GBOTB.extended.tre), which was derived from two recently published mega‐trees and includes 74 533 species and all families of extant vascular plants, is the largest dated phylogeny for vascular plants. V.PhyloMaker can generate phylogenies for very large species lists (the largest species list that we tested included 314 686 species). V.PhyloMaker generates phylogenies at a fast speed, much faster than other phylogeny‐generating packages. Our tests of V.PhyloMaker show that generating a phylogeny for 60 000 species requires less than six hours. V.PhyloMaker includes an approach to attach genera or species to their close relatives in a phylogeny. We provide a simple example in this paper to show how to use V.PhyloMaker to generate phylogenies.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.04434

V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants

An updated megaphylogeny of plants, a tool for generating plant phylogenies, and an analysis of phylogenetic community structure

The diversity of a region reflects both local diversity and the turnover of species (beta diversity) between areas. The angiosperm flora of eastern Asia (EAS) is roughly twice as rich as that of eastern North America (ENA), in spite of similar area and climate. Using province/state-level angiosperm species floras, we calculated beta diversity as the slope of the relationship between the log of species similarity (S) and either geographic distance or difference in climate. Distance-based beta diversity was 2.6 times greater in the north‐south direction in EAS than in ENA and 3.3 times greater in the east‐west direction. When ln S was related to distance and climate difference in multiple regressions, both distance and climate PC1 were significant effects in the north‐south direction, but only geographic distance had a significant, unique influence in the east‐ west direction. The general predominance of distance over environment in beta diversity suggests that history and geography have had a strong influence on the regional diversity of these temperate floras.

/pdf/beta-diversity-of-angiosperms-in-temperate-floras-of-eastern-565jsc37r4.pdf

Beta diversity of angiosperms in temperate floras of eastern Asia and eastern North America

Species turnover, or beta diversity, has been predicted to decrease with increasing latitude, but few studies have tested this relationship. Here, we examined the beta diversity-latitude relationship for vascular plants at a continental scale, based on complete species lists of native vascular plants for entire states or provinces in North America (north of Mexico). We calculated beta diversity as the slope of the relationship between the natural logarithm of the Jaccard index (lnJ ) for families, genera or species, and both geographic distance and climate difference within five latitude zones. We found that beta diversity decreased from south to north; within latitude zones, it decreased from species to genera and families. Geographic and climatic distance explained about the same proportion of the variance in lnJ in zones south of c. 50 degrees N. North of this latitude, nearly all the explained variance in lnJ was attributable to geographic distance. Therefore, decreasing beta diversity from south to north reflects decreasing climate differentiation within more northerly latitude zones, and primarily post-glacial dispersal limitation north of 50 degrees N.

Hong Qian

Papers

Large-scale processes and the Asian bias in species diversity of temperate plants

V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants

An updated megaphylogeny of plants, a tool for generating plant phylogenies, and an analysis of phylogenetic community structure

Beta diversity of angiosperms in temperate floras of eastern Asia and eastern North America

A latitudinal gradient in large‐scale beta diversity for vascular plants in North America