A multi-locus time-calibrated phylogeny of the siphonous green algae

Abstract

The siphonous green algae are an assemblage of seaweeds that consist of a single giant cell. They comprise two sister orders, the Bryopsidales and Dasycladales. We infer the phylogenetic relationships among the siphonous green algae based on a five-locus data matrix and analyze temporal aspects of their diversification using relaxed molecular clock methods calibrated with the fossil record. The multi-locus approach resolves much of the previous phylogenetic uncertainty, but the radiation of families belonging to the core Halimedineae remains unresolved. In the Bryopsidales, three main clades were inferred, two of which correspond to previously described suborders (Bryopsidineae and Halimedineae) and a third lineage that contains only the limestone-boring genus Ostreobium. Relaxed molecular clock models indicate a Neoproterozoic origin of the siphonous green algae and a Paleozoic diversification of the orders into their families. The inferred node ages are used to resolve conflicting hypotheses about species ages in the tropical marine alga Halimeda.

Introduction

The siphonous green algae form a morphologically diverse group of marine macroalgae. They are readily distinguished from other green algae by their ability to form large, differentiated thalli comprised of a single, giant tubular cell. This tubular cell branches and fuses in various patterns to form a broad range of forms (Fig. 1). Individual branches of the tubular cell are called siphons. The siphonous green algae include two sister orders (Bryopsidales and Dasycladales) and belong to the chlorophytan class Ulvophyceae. The Cladophorales, an order closely related to the Bryopsidales and Dasycladales (Zechman et al., 1990), is sometimes included in the siphonous algae but its members are not truly siphonous because they are generally multicellular. The siphonous green algae are unique among their chlorophytan relatives in having a relatively rich fossil record because many of them biomineralize.

The Bryopsidales range in morphology from simple, branched thalli (Fig. 1A and B) to more complex organizations with interwoven siphons, differentiated thalli and various morpho-ecological specializations (Fig. 1C–F). They have multiple nuclei scattered throughout the siphons. These algae form an important component of the marine flora, particularly in tropical marine environments, where they are among the major primary producers on coral reefs, in lagoons and seagrass beds. They comprise roughly 500 recognized species (Guiry and Guiry, 2008). The calcified representatives are major contributors of limestone to coral reef systems and are well-represented in the fossil record (Hillis-Colinvaux, 1986, Mu, 1990). The Bryopsidales are also common in warm-temperate marine habitats where they form a significant component of the flora (e.g., Codium). Several bryopsidalean taxa are vigorous invasive species (e.g., Codium fragile, Caulerpa taxifolia and Caulerpa racemosa var. cylindracea) that are known to have profoundly affected the ecology and native biota in areas of introduction. Molecular phylogenetic studies have shown two principal bryopsidalean lineages, both comprising simple as well as complex forms (Lam and Zechman, 2006, Verbruggen et al., 2009, Woolcott et al., 2000).

Extant Dasycladales are characterized by a central axis surrounded by whorls of lateral branches (Fig. 1G–J). Members of this group contain a single giant nucleus situated in the rhizoid during the vegetative phase of their life cycle. Albeit relatively inconspicuous, they are common algae of shallow tropical and subtropical marine habitats. Both calcified and non-calcified representatives have left a rich fossil record dating back to the Cambrian Period (540–488 my) (Berger and Kaever, 1992, LoDuca et al., 2003). Fossil remains suggest that non-calcified dasyclads were most diverse during the Ordovician and Silurian periods and declined in favor of calcified representatives after the Early Devonian (±400 my), perhaps as a result of selection for resistance to herbivory (LoDuca et al., 2003). In all, over 700 species are known from the fossil record, and fossil dasyclads are important tools for both biostratigraphic and paleoenvironmental studies (Berger and Kaever, 1992, Bucur, 1999). The present dasycladalean diversity consists of 37 species belonging to 10 genera and the two families Dasycladaceae and Polyphysaceae (Berger, 2006). Molecular phylogenetic studies have shown that the Polyphysaceae arose from the Dasycladaceae, leaving the latter paraphyletic (Berger et al., 2003, Olsen et al., 1994, Zechman, 2003).

Currently available phylogenetic studies of the siphonous green algae suffer from a few shortcomings. First, the studies have been based on single loci, yielding partially resolved trees with some unresolved taxa. Second, several important groups within the Bryopsidales have not been included. Finally, the temporal aspects of siphonous green algal diversification have not been explored in sufficient detail. Several recent studies point to the necessity of a time-calibrated phylogenetic framework. For example, the large discrepancy between species ages resulting from interpretations of molecular data and the fossil record creates confusion (Dragastan et al., 2002, Kooistra et al., 2002). Furthermore, biogeographic interpretations are difficult without reference to a temporal framework (Verbruggen et al., 2005, Verbruggen et al., 2007). So far, the fossil record has been used on one occasion to calibrate a dasycladalean molecular phylogeny in geological time (Olsen et al., 1994). In the years that have passed since the publication of this study, however, several important discoveries have been made in dasyclad paleontology (e.g., Kenrick and Li, 1998, LoDuca et al., 2003) and more advanced calibration methods have been developed (reviewed by e.g., Verbruggen and Theriot, 2008).

The present study sets out to achieve two goals. First, it aims to resolve the phylogeny of the siphonous green algae more fully and include previously omitted taxonomic groups. Second, it aspires to provide a temporal framework of siphonous green algal diversification by calibrating the phylogeny in geological time using information from the fossil record. Our approach consists of model-based phylogenetic analyses of a five-locus alignment spanning both of the orders and uses a composite (partitioned) model of sequence evolution. Calibration of the phylogeny in geological time is achieved with Bayesian implementations of relaxed molecular clock models, using a selection of fossil reference points.