Multi-locus phylogeny and divergence time estimates of Enallagma damselflies (Odonata: Coenagrionidae)

Highlights

• Enallagma damselflies show complex diversification across North America and Eurasia.

• Four subclades radiated in the Pleistocene to produce 28 extant species.

• Both speciation and extinction rates increased over the last 1.5 million years.

Abstract

Reconstructing evolutionary patterns of species and populations provides a framework for asking questions about the impacts of climate change. Here we use a multilocus dataset to estimate gene trees under maximum likelihood and Bayesian models to obtain a robust estimate of relationships for a genus of North American damselflies, Enallagma. Using a relaxed molecular clock, we estimate the divergence times for this group. Furthermore, to account for the fact that gene tree analyses can overestimate ages of population divergences, we use a multi-population coalescent model to gain a more accurate estimate of divergence times. We also infer diversification rates using a method that allows for variation in diversification rate through time and among lineages. Our results reveal a complex evolutionary history of Enallagma, in which divergence events both predate and occur during Pleistocene climate fluctuations. There is also evidence of diversification rate heterogeneity across the tree. These divergence time estimates provide a foundation for addressing the relative significance of historical climatic events in the diversification of this genus.

Introduction

Accurate estimation of divergence times is essential to understanding many evolutionary processes. Time-calibrated phylogenies are important for answering questions about a variety of topics such as biogeography, estimation of diversification rates, and phenotypic evolution. One particular area of interest is how recent climatic changes have influenced the diversification of taxa. The Earth’s climate has experienced fluctuations throughout its history. The magnitude of these fluctuations on biological diversity is of great interest as we move toward a better understanding of anthropogenic climate change.

Previous research has demonstrated that climatic fluctuations during the Quaternary have left distinct genetic signatures across a variety of biota (Hewitt, 2000, Hewitt, 2004). While there were repeated glacial advances and retreats, impacts from these Pleistocene fluctuations should be more pronounced within the last 0.7 million years, a period of more intense glacial cycles (Webb and Bartlein, 1992). These repeated cycles are thought to have promoted divergence in many taxa (Knowles, 2001, Carstens and Knowles, 2006, Mila et al., 2007, Shepard and Burbrink, 2009, Niemiller et al., 2012). However, few studies have focused on obtaining accurate divergence dates to verify that speciation events coincide with major climatic events.

Estimating time-calibrated phylogenies is notoriously difficult, but recent advances in “relaxed-clock” models have led to more accurate estimates of divergence times (Thorne and Kishino, 2002, Sanderson, 2003, Drummond et al., 2006, Drummond and Rambaut, 2007). Although it has been well known for decades that a gene tree may be different from the species tree, most of these divergence time methods were applied to a single gene tree, or to a concatenated data matrix of multiple genes. Recent advances allow joint estimation of a set of gene trees within a shared species tree using a multispecies coalescent model. A commonly used method, ∗BEAST, uses a fully Bayesian framework to estimate the species tree (Heled and Drummond, 2010). This method allows for estimation of divergence times on the species tree and thus more accurate estimates of divergence times can be obtained.

With 38 described species, Enallagma damselflies (Zygoptera:Coenagrionidae) are one of the most diverse groups of Odonata in North America (Westfall and May, 2006). Previous phylogenetic analyses based on mitochondrial DNA and morphological data have consistently separated this genus into two major clades, the “Northern” and “Southern” clades, indicating where the centers of diversity for each is greatest (Northeastern U.S. versus Southeastern U.S., respectively) (Brown et al., 2000, Turgeon et al., 2005). Using a strict molecular clock with a rate of sequence divergence of 2.3% per million years based on Brower’s insect mtDNA clock (Brower, 1994), the last common ancestor of these two major clades was estimated to be approximately 15 million years ago (Turgeon et al., 2005). The Northern clade is composed of three recent radiations (<250,000 years) whereas the Southern clade is composed of mostly older species. Additionally, the estimated diversification rates increased in the last million years by ∼24x in the Northern clade versus only ∼6× in the Southern clade (Turgeon et al., 2005). These results suggest that the Pleistocene glacial cycles had a profound effect on the diversification of this genus.

In this study we expand on the mtDNA dataset of Turgeon et al. (2005) with nuclear loci and analyze these data with a multispecies coalescent approach to gain more robust estimates of divergence dates. Additionally, we infer species diversification rates through time using the estimated time-calibrated species tree. This will allow for a better understanding of the impact of Quaternary climatic oscillations on the diversification of this genus of damselflies in North America.