The emerging field of geogenomics: Constraining geological problems with genetic data

Abstract

The development of a genomics-derived discipline within geology is timely, as a result of major advances in acquiring and processing geologically relevant genetic data. This paper articulates the emerging field of “geogenomics”, which involves the use of large-scale genetic data to constrain geological hypotheses. The paper introduces geogenomics and discusses how hypotheses can be addressed through collaboration between geologists and evolutionary biologists. As an example, geogenomic methods are applied to evaluate competing hypotheses regarding the timing of the Andean uplift, the closure of the Isthmus of Panama, the onset of trans-Amazon drainage, and Quaternary climate variation in the Neotropics.

Introduction

In the past decade, DNA sequencing of plant and animal taxa (Box 1) has generated vast amounts of genetic data. In light of advancing technologies, it is certain that data collection will compound exponentially, and it is conceivable, even likely, that complete genomes of taxa from across the tree of life will become available in the next decade. Genetically distinct populations and species arise in response to environmental variation as a consequence of evolutionary processes, such as natural selection; conversely the genetic composition of modern taxa retains information about their environmental past. As a result of this linkage between genetic composition and environmental history, phylogenetics (Box 2) represents a major opportunity for qualitative advance in geologic reconstruction, particularly given the development of new bioinformatics approaches for the collection and interpretation of large genetic data sets. In this paper, biologists and geologists collaborate to envision an emergent field called “geogenomics”, which we define as the use of large-scale genetic data to test or constrain geological hypotheses (Fig. 1). By imagining this future, we hope to hasten its realization and illuminate possible pitfalls in its application. We anticipate that geogenomics will be most useful for (1) providing an independent chronology for a variety of past geologic events, some of which may be otherwise extremely difficult or impossible to date, and (2) providing constraint and nuance to paleo-environmental interpretations.

Geogenomics is deeply rooted in the field of biogeography. From its earliest history (Wallace, 1852), biogeographers sought patterns in the distribution of plant and animal taxa to infer their geographic history and related these patterns to the geological processes that shaped their evolution. Geological processes that produce vicariance – isolation of populations in response to the formation of a geographic barrier to migration and consequent genetic divergence between these populations – are central in biogeography as drivers of evolutionary change.

Cladistic or phylogenetic biogeography (focused above the species level) and phylogeography (focused within or among closely related species) introduced phylogenies into biogeographic analyses. Time-calibrated phylogenies (Fig. 2) are used to determine if clades arose through vicariance or if they attained disjunct (fragmented) distributions by dispersing across geographic barriers. Comparing the age of disjunction with the accepted age of barrier formation can help to constrain these alternative hypotheses. Hence, in these disciplines geologic information is used to constrain evolutionary histories (Fig. 1).

Whereas the concept of “reciprocal illumination” (Hennig, 1966), when applied to historical biogeography, describes the search for congruence between phylogenetic hypotheses and earth history, geogenomics encourages the flow of information from biology to geology. Thus, it builds upon the historic use of biotic patterns to infer geologic processes, such as the distribution of the Glossopteris flora and Permo-Triassic vertebrates, which contributed to the development of plate tectonics (Wegener, 1924). Geogenomics is timely, because of recent advances in methodologies used to obtain and analyze phylogenetic data. In particular, novel platforms for DNA sequencing (“next generation” approaches) can rapidly provide millions of DNA sequences from non-model organisms (see Supplementary Information). The profusion of genomic data and new bioinformatics methods promises greater phylogenetic precision and the ability to address novel questions of interest to biologists and geologists.

In this paper we present four examples of outstanding geological problems that have been addressed by classical geological methods, but only recently by biogeographic or phylogenetic methods that provide new insight. In each case we briefly review the problem and alternative explanatory hypotheses. Exemplary published biological studies are presented, followed by our own suggestions for possible future geogenomic research. Key vocabulary (bolded text) and concepts (italicized text) are defined in boxes, and additional detail about methods for geogenomic hypothesis testing is provided in the Supplementary Information. All of our examples are taken from the New World tropics, but the global generality of these methods should be clear to all readers.