In Phylogenetic Ecology, Nathan G. Swenson synthesizes this nascent field’s major conceptual, methodological, and empirical developments to provide students and practicing ecologists with a foundational overview. Along the way, he highlights those realms of phylogenetic ecology that will likely increase in relevance—such as the burgeoning subfield of phylogenomics—and shows how ecologists might lean on these new perspectives to inform their research programs.
In Phylogenetic Ecology, Nathan G. Swenson synthesizes this nascent field’s major conceptual, methodological, and empirical developments to provide students and practicing ecologists with a foundational overview. Along the way, he highlights those realms of phylogenetic ecology that will likely increase in relevance—such as the burgeoning subfield of phylogenomics—and shows how ecologists might lean on these new perspectives to inform their research programs.
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Overview
In Phylogenetic Ecology, Nathan G. Swenson synthesizes this nascent field’s major conceptual, methodological, and empirical developments to provide students and practicing ecologists with a foundational overview. Along the way, he highlights those realms of phylogenetic ecology that will likely increase in relevance—such as the burgeoning subfield of phylogenomics—and shows how ecologists might lean on these new perspectives to inform their research programs.
Product Details
| ISBN-13: | 9780226671642 |
|---|---|
| Publisher: | University of Chicago Press |
| Publication date: | 11/22/2019 |
| Sold by: | Barnes & Noble |
| Format: | eBook |
| Pages: | 240 |
| File size: | 2 MB |
About the Author
Read an Excerpt
CHAPTER 1
Introduction and a Brief Phylogenetics Primer
The fields of ecology, evolution, and biogeography were neatly intertwined over a century ago. However, they became more compartmentalized approximately midway through the twentieth century. In the past few decades, there has been a renewed interest in the integration of evolutionary history into ecology and vice versa. Running throughout this literature from a century ago until now has been phylogenetic information in one form or another. This phylogenetic thread constitutes what I call phylogenetic ecology, and it is the topic of this book.
The use of phylogenetic information in ecology is now often touted as a means to integrate evolutionary history into ecology (Cavender-Bares et al. 2009; Cadotte and Davies 2017). However, the ways in which phylogenies have been used in ecology are much more diverse. Phylogenies, or more precisely measures of relatedness, were originally utilized in ecology as proxies for the similarity of species, and a tradition of using phylogenies in this fashion continues to this day in ecology (Jaccard 1901; Elton 1946; Jarvinen 1982; Webb 2000). Phylogenies have also been used in ecology for topics ranging from the inferring of historical biogeography (Brooks 1985; Brooks and Wiley 1986; Brooks and McLennan 1991; Losos 1996; Losos et al. 1998) and the assembly of lineages to considering phylogenetic nonindependence in comparative analyses (Felsenstein 1985; Harvey and Pagel 1991) to quantifying phylogenetic diversity in order to set conservation priorities (Faith 1992, 1996; Baker 2002).
The first goal of this book is to guide the reader through the history of phylogenetic ecology. I begin with phylogenetic nonindependence and comparative methods, despite this not being the first way in which phylogenies were integrated into ecology. I do this and provide a primer on phylogenetic inference at the end of this chapter because a firm understanding of phylogenies and comparative methods allows one to properly grasp and interpret that work that led up to these developments and the work since. At this point, I should note that while this book is written primarily for an entry-level researcher that is interested in learning more about how phylogenies have, can, and should be integrated into ecology, it is my hope that the book will also be of interest to the more seasoned phylogenetic ecologist that may or may not appreciate my viewpoint. Thus, I have taken the approach of focusing on core concepts, methods, and topics and major developments. The examples I provide in the text do not constitute a comprehensive treatment of all work on that topic. Rather, I sought to provide a digestible volume that will spur on the interests of a novice reader. I therefore apologize in advance to any colleagues that are dismayed that I did not discuss their work or highlight their work more prominently.
The second goal of this book is to lay out the field of phylogenetic ecology such as it is and then to challenge the field to reconsider how we think about and utilize phylogenies in ecology. My suggestions for a remodeling of phylogenetic ecology arise from my concern for the current state of the field. Over the past decade, phylogenetic ecology has experienced unwarranted euphoria all the way to unwarranted depression. At present, many have pushed phylogenetic ecology aside as a fad or bandwagon that overly relied on phylogenies as a proxy for ecological similarity, while others still believe that phylogenies contain a great deal of useful information that can't be captured via other data sources. I am not convinced that either of these opinions are well grounded (Swenson 2011a, 2013, 2014a). Furthermore, almost all phylogenetic approaches in ecology being employed at present actually fail to do the one thing most say they want to accomplish: integrate evolutionary history into ecology. For example, correlating phylogenetic diversity with an ecological variable is, at best, a weak integration of evolutionary history into ecology, as we know next to nothing about the evolutionary history of the lineages (e.g., the tempo and mode of trait evolution, biogeographic history) and how that history actually impacts ecological interactions. Thus, phylogenetic information should play an important role in ecology, but how phylogenetic information is currently utilized in ecology does not align with this role.
The remodeling of phylogenetic ecology that I propose should have five foci. First, phylogenetic nonindependence or phylogenetic signal in ecological data can be quantified, at least crudely, in most systems of study. This signal should be measured, and phylogenetically informed statistical methods should be employed. Second, measures of phylogenetic diversity are useful for setting conservation priorities and as very quick indicators that something about relatedness is correlated with the ecological pattern or process of interest. However, phylogenetic diversity itself, no matter how we slice and dice it, will never tell us why phylogeny or evolutionary history is related to the ecological pattern or process of interest. Even in those cases where it is more strongly correlated with a variable other than independent variables, we will not know why, and an assumption that there is a phylogenetically conserved trait driving the relationship is not necessarily true. Third, phylogenies should no longer be used as proxies for ecological similarity. Again, they may give basic initial insights into the diversity in ecological assemblages, but we don't know why a given phylogenetic pattern exists. Fourth, phylogenies are best employed in ecology as backbone pieces of data upon which biogeographic and trait information can be draped. When phylogenies are used in this manner, evolutionary history is truly being integrated into ecology. There is a strong literature that uses the phylogenies in this manner, but it is now often forgotten about in phylogenetic ecology. Fifth, phylogenies are best used for regional- and global-scale studies that elucidate the drivers of regional- and global-scale assemblage composition and diversity. However, we must also strive to elucidate how local-scale ecological interactions feedback to influence these larger-scale processes (i.e., the feedbacks between macro- and microevolution).
If phylogenetic ecology could remodel itself to focus on these five items, then it has tremendous promise to propel the integration of ecology and evolutionary history. A failure to do so will likely result in phylogenetic information being relegated to the backwaters of ecology, where its potential will not be realized. In formulating this remodeling, I have had to confront many issues. First and foremost, I have certainly violated many of the rules I suggest we follow under the remodeling proposed (e.g., Swenson et al. 2006, 2007). Some of this was due to my zeal for using phylogenies, and some of it was due to my desire to obtain more information about the species we study and not being satisfied with only analyzing species names. I do still contend that analyzing species lists and abundance distributions is less powerful than analyzing the phylogenetic composition of ecological systems. However, I have come to realize that phylogenetic information can be better employed in ecology. I have known this for a while, but have been confronted with a second issue. That issue is that the remodeling of phylogenetic ecology requires the generation of phylogenies with dense taxonomic sampling. This is not a trivial problem. Indeed, in some instances, the approaches I suggest almost demand a fully resolved tree of life. We aren't there yet, but the technology, tools, and databases available are getting to a point where well-sampled phylogenies for most to all major lineages in assemblages are possible (e.g., Hinchliff et al. 2015; Kumar et al. 2017). In sum, the remodeling I propose is not an easy route, but it is, I think, the necessary route for phylogenetic ecology to remain an interesting field of investigation.
1.1. Chapter Breakdown and Progression
The book progresses from phylogenetic terminology, inference, and nonindependence to community phylogenetics and phylogenetic analyses of big data. In the sections that follow in this chapter, I will provide a very simplistic entryway and general introduction to phylogenetic trees for ecologists. Although most students in ecology roughly know what phylogenetic trees do and do not represent, many are hard pressed to explain exactly what data are used to infer them and how they are inferred and interpreted. The goal of these sections is to fill this void and place all readers on the same footing. I will begin with a basic tour of phylogenetic trees, including their structure and specific terminology related to this structure. Once this understanding is achieved, the chapter will move on to give a general overview of how phylogenies are inferred — data types, assumptions, and methods. It is impossible to cover the breadth of phylogenetic theory and inference in a single chapter, and this chapter is not designed to be such a reference. Rather, it is simply meant to set a baseline understanding of how to "read" phylogenies, learn generally how they are made, and recognize what information they do and do not contain.
In chapter 2, we will discuss phylogenetic nonindependence, comparative methods, and the analysis of phylogenetic signal and niche conservatism. Comparative analyses of data from across regions and clades play a critical role in modern ecology, and they have been at the core of many important past developments and syntheses. The robustness of such analyses critically relies on statistical approaches that account for the shared evolutionary history, and therefore statistical nonindependence, of the lineages being investigated (Felsenstein 1985). Phylogenetically informed comparative methods have a long and hotly debated history in ecology (e.g., Ackerly and Donoghue 1995; Harvey et al. 1995; Westoby et al. 1995a, 1995b; Rohlf 2006). There have been many misunderstandings, misconceptions, misapplications of, and downright disdain for phylogenetic information in comparative ecology. I begin the second chapter by discussing, briefly, some of this rocky history and how the lack of phylogenetic information in the past has freed researchers from having to explicitly consider phylogenetic nonindependence in their data sets. However, I quickly transition to the fact that phylogenetic information is now widely available, albeit often in crude form, and should be used in all modern comparative ecology either by using it to analyze data already collected or by using it to design experiments (Weber and Agrawal 2012). I then cover the major classes of phylogenetic comparative methods, the conceptual foundation of the methods, and how they are implemented in practice. The ultimate goals of the chapter are to move the reader away from thinking of phylogenetic nonindependence as a nuisance and toward using powerful phylogenetic comparative methods as a standard approach in their analytical toolbox. Next, I will discuss the measurement of phylogenetic signal and niche conservatism and how and why it has become of interest to ecologists. Throughout this discussion, I seek to link concepts, definitions, and research questions and highlight those instances where, I think, the literature could course correct.
In chapter 3, I focus on the rapidly growing phylogenetic diversity literature. I start with work from the early 1990s where the measurement of phylogenetic diversity became popularized as an additional metric of biological diversity for conservation purposes (Faith 1992, 1996). As phylogenetic information has become more available, measures of phylogenetic diversity, based upon phylogenetic branch lengths, have become more common in the literature (Cavender-Bares et al. 2009). At present, measures of phylogenetic diversity are used as key pieces of information in studies ranging from conservation biology (Vane-Wright et al. 1991; Faith 1992, 1996; Winter et al. 2013) to species coexistence to biodiversity-ecosystem functioning relationships (Cadotte et al. 2008, 2009; Flynn et al. 2011; Srivastava et al. 2012). While phylogenetic diversity itself is fairly easy to conceptualize, in practice there are many metrics of phylogenetic diversity. These metrics can be independent of one another or monotonic, often making it difficult to compare the results of different studies and to achieve a synthesis (Vellend et al. 2011; Swenson 2011b; Tucker and Cadotte 2013; Swenson 2014a; Tucker et al. 2017). This chapter will provide a history of measures of phylogenetic diversity in ecology. An emphasis will be placed on how they are quantified, but more importantly, the text will also explore important conceptual and biological differences between different metrics.
In chapter 4, I discuss one of the two major approaches for integrating phylogenetic information into community ecology, which I term the phylogenetic proxy approach (Swenson 2013). The use of phylogenetic information to understand community assembly and structure has a long history. Early work relied on relatedness as a proxy for ecological similarity, where co-occurring congeners were believed to reflect the importance of the abiotic filtering of similar phenotypes and a lesser role for biotic interactions, such as interspecific competition (Jaccard 1901; Palmgren 1921). This research approach, which computed taxonomic ratios (e.g., the number of genera: the number of species in a community), led to a rather large literature and some classic debates in ecology regarding the usage of null models (e.g., Simberloff 1970), but it had largely died out by the 1990s. However, Cam Webb's seminal work in the American Naturalist in 2000 (Webb 2000), which introduced phylogenetic branch lengths to calculate the degree of relatedness in communities instead of taxonomic ratios, reignited this realm of research, leading to hundreds of articles and the formation of what is now known as "community phylogenetics." The lynchpin of the community phylogenetics research program rests upon the assumption that phylogenetic relatedness is a robust proxy of ecological similarity. Not long after Webb's paper, researchers began to highlight the frequency at which this assumption is not met and the implications of this for inferences regarding the processes driving community assembly and structure (e.g., Cavender-Bares et al. 2004; Losos 2008). The present work describes this entire historical development and discusses the current state of the field of community phylogenetics. Critically, at the end of the chapter, I discuss several major conceptual challenges facing this field and discuss whether the field should hasten its movement away from using the phylogeny as a proxy for similarity and toward using it as a backbone piece of information.
In chapter 5, I discuss the second major approach to integrating phylogenetic information into community ecology, which I call the phylogeny as a backbone approach. The previous chapter covered the historical development and current usage of phylogenetic relatedness as a proxy for ecological similarity in community ecology research. The chapter ends with an argument that in most cases, we should move away from using the phylogeny as a proxy for similarity and toward using it as a backbone onto which we should drape data. Chapter 5 seeks to reinforce and expand this argument by first discussing the development of phylogenetic community ecology where spatial and trait information has been placed onto a phylogeny to make robust inferences regarding the ecological and evolutionary processes underlying the historical assembly and present-day structure of ecological communities. Examples will be drawn from "classic" systems where researchers have successfully and clearly linked evolutionary history with community assembly (e.g., Losos et al. 1998; Gillespie 2004). The chapter will end with an argument that the most interesting and informative future integrations of phylogenetic information into community ecology will come from utilizing phylogenies as backbones and not proxies.
Chapter 6 is a discussion of how phylogenetic information is utilized to ask large-scale ecological questions regarding the drivers of regional- to global-scale patterns of species assemblage composition and diversity. Specifically, I will discuss the latitudinal species diversity gradient with respect to the niche conservatism (Wiens and Donoghue 2004) and cradles versus museums hypotheses (e.g., Stebbins 1974; Stenseth 1984; Chown and Gaston 2000) and how phylogenetic information is critical for robust tests of these hypotheses. I will also discuss the assembly of regional-scale floras and faunas with respect to the timing of lineage diversification, priority effects, and ecological opportunity. A final goal of this chapter is to elucidate the linkages between phylogenetic analyses at global and regional scales to community-scale analyses that utilize a phylogenies as a backbone approach.
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Table of Contents
Preface1. Introduction and a Brief Phylogenetics Primer
2. Phylogenetic Nonindependence, Comparative Ecology, and Phylogenetic Conservatism
3. The Measurement of Phylogenetic Diversity
4. Community Assembly: Phylogenies as a Proxy
5. Community Assembly: Phylogenies as a Backbone
6. Global Patterns of Biodiversity, Diversification, Conservatism, and Priority
7. Functional Phylogenomics for Ecology
8. Building Trees for Every System and Scale and Biodiversity Informatics
9. Conclusions and Remodeling Phylogenetic Ecology
References
Index