Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny

Abstract

An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. However, many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often undersampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing expressed sequence tag, mitochondrial genome, nuclear genome, and ribosomal DNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, and Pentastomida); Multicrustacea (Copepoda, Malacostraca, and Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, and Branchiopoda). Within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Branchiopoda + Cephalocarida as the sister group of hexapods. In multiple different analyses, we see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. However, when we analyze the same set of species and ignore rate of gene evolution, we find higher support when including all data, more in line with a "total evidence" philosophy. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylogenetic insights into long-standing questions, especially when carefully analyzed in combination with other data.

On the phylogenetic position of Pseudophilomedinae within Sarsielloidea (Ostracoda, Myodocopida), with a description of one new Harbansus from Ningaloo Reef and redescription of H. paucichelatus from Yucatan

“…The results of our molecular phylogenetic analyses are in accordance with Oakley (2005), Oakley and Cunningham (2002), and Oakley et al (2012) indicating polyphyly of Philomedidae (Figs. 11, 12).…”

“…In the analysis of 18S, we have chosen three outgroup species, Vargula hilgendorfii Müller, 1986, V. tsujii Baker, 1977, andMelavargula japonica Poulsen, 1962, and only the first one in the molecular analysis of 28S. They belong to the superfamily Cypridinoidea, which has been shown in previous molecular analysis (Oakley 2005;Oakley and Cunningham 2002;Oakley et al 2012) to be the sister taxon of Sarsielloidea. Sequences for all three outgroup species, and another 30 highly similar sequences, all belonging to the superfamily Table 1).…”

“…Recent molecular studies (Oakley 2005;Oakley and Cunningham 2002;Oakley et al 2012) show that the phylogenetic relationships between the three Sarsielloidea families are not resolved, because some Sarsiellidae cluster with some Philomedidae, while other Philomedidae cluster with Rutidermatidae. However, these authors did not discuss morphological characters that may support these phylogenies, but instead call for better taxon sampling.…”

Arthropod fossil data increase congruence of morphological and molecular phylogenies

“…The latter is supported by a number of independent lines of evidence, including nuclear ribosomal genes 8,15 , mitochondrial genomes and gene order, nuclear protein-coding genes 1 and transcriptomics [2][3][4] , but has so far remained elusive in morphological phylogenies, apart from those based solely on neural characters 16 , which resolve malacostracan crustaceans closer to hexapods than to branchiopods. The position of the pycnogonids is equally controversial, being variously resolved as the closest relatives of euchelicerates 1,3,15 (Fig.…”

“…1): pycnogonids (sea spiders), euchelicerates (horseshoe crabs and arachnids), myriapods (centipedes and millipedes), hexapods (insects and their flightless relatives) and crustaceans (crabs, lobsters, barnacles and so on). Each group is characterized by a distinct set of morphological features and their monophyly is little disputed, except for the crustaceans [1][2][3][4] . Molecular clock estimates calibrated by new fossil discoveries indicate that these groups originated and had begun to diversify by at least the midCambrian 5 .…”