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

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 phylo- genetic insights into long-standing questions, especially when carefully analyzed in combination with other data

An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida)

BACKGROUND: Glass sponges (Class Hexactinellida) are important components of deep-sea ecosystems and are of interest from geological and materials science perspectives. The reconstruction of their phylogeny with molecular data has only recently begun and shows a better agreement with morphology-based systematics than is typical for other sponge groups, likely because of a greater number of informative morphological characters. However, inconsistencies remain that have far-reaching implications for hypotheses about the evolution of their major skeletal construction types (body plans). Furthermore, less than half of all described extant genera have been sampled for molecular systematics, and several taxa important for understanding skeletal evolution are still missing. Increased taxon sampling for molecular phylogenetics of this group is therefore urgently needed. However, due to their remote habitat and often poorly preserved museum material, sequencing all 126 currently recognized extant genera will be difficult to achieve. Utilizing morphological data to incorporate unsequenced taxa into an integrative systematics framework therefore holds great promise, but it is unclear which methodological approach best suits this task. RESULTS: Here, we increase the taxon sampling of four previously established molecular markers (18S, 28S, and 16S ribosomal DNA, as well as cytochrome oxidase subunit I) by 12 genera, for the first time including representatives of the order Aulocalycoida and the type genus of Dactylocalycidae, taxa that are key to understanding hexactinellid body plan evolution. Phylogenetic analyses suggest that Aulocalycoida is diphyletic and provide further support for the paraphyly of order Hexactinosida; hence these orders are abolished from the Linnean classification. We further assembled morphological character matrices to integrate so far unsequenced genera into phylogenetic analyses in maximum parsimony (MP), maximum likelihood (ML), Bayesian, and morphology-based binning frameworks. We find that of these four approaches, total-evidence analysis using MP gave the most plausible results concerning congruence with existing phylogenetic and taxonomic hypotheses, whereas the other methods, especially ML and binning, performed more poorly. We use our total-evidence phylogeny of all extant glass sponge genera for ancestral state reconstruction of morphological characters in MP and ML frameworks, gaining new insights into the evolution of major hexactinellid body plans and other characters such as different spicule types. CONCLUSIONS: Our study demonstrates how a comprehensive, albeit in some parts provisional, phylogeny of a larger taxon can be achieved with an integrative approach utilizing molecular and morphological data, and how this can be used as a basis for understanding phenotypic evolution. The datasets and associated trees presented here are intended as a resource and starting point for future work on glass sponge evolution

Evolutionary inference for functional data: using Gaussian processes on phylogenies of functional data objects

This thesis explores the use of phylogenetics and functional data analysis for the analysis of continuous ancestral data such as continuous curves. Gaussian processes (GPs) are placed on phylogenies in order to perform evolutionary inferences on the functional data objects. The mean and covariance functions of the GP model the relationships between different states on the phylogeny. The functional data objects are completely described by the spatial and temporal parameters within the covariance functions, allowing inferences to be made, for example, by the method of maximum likelihood estimation. Inferences are successfully made on known phylogenies, phylogenies with missing ancestral data and on phylogenies of unknown topology. This work is potentially useful for those wanting to compute evolutionary inferences on continuous ancestral data, for which phylogenetic GPs are shown to be an efficient and promising tool

Morphological Cladistic Analysis of the Cordaitean Cones and Implications for Plant Lineages

The cordaiteans were a group of Carboniferous and Permian woody plants, which thrived in wetlands and thrived in wetlands and terra firma habitats. Cordaitean cones from wetland habitats are exquisitely well preserved and contain a suit of characters that make their fossils prime candidates for cladistic analysis; historically, there are more male cones than female cone. Cordaitean morphological characteristics make this clade a possible precursor lineage of modern conifer and gnetalean lineages. However, the exact relation between fossil seed-plant clades and modern gymnosperm groups remains enigmatic. The resent discovery of a bisexual cordaitean cone calls into question the relationship between cordaiteans, gnetaleans and angiosperms. This study performs three cladistics analyses in order to find the relations of taxa within the cordaitean clade and other early plant lineages using primarily PAUP* and TNT. An analysis of male only cones provides a phylogram for the relations between the corditean taxa; the results also suggest a bisexual ancestry for the clade. A second analysis attempted to introduce the morphologically distinct female cones; the results produce a similar strict consensus tree. However, many of the female cones do not pair with their associated male cones indentified in ‘whole-plant’ reconstructions of cordaitean lineages. Instead, female cones formed separate linages. A final analysis incorporated other plant lineages and assigned traits associated with seeds and pollen to both male and female cones. The results support an early bisexual ancestry to the cordaiteans, and suggests that the cordaiteans are a polyphylecit clade, which gave rise to the voltzialean-conifer lineage. Including more fossil taxa lineages may prove useful, as well as establishing other criteria to compare characters to taxa in cladistics analysis

Developments for the Next Generation of Evolutionary Paleobiology

During the modern synthesis, researchers merged insights from natural history, evolutionary genetics, and paleontology to develop a cohesive theoretical foundation for evolutionary theory. Since then, the rapid emergence of genomic resources has revolutionized our understanding of evolutionary processes. Despite neontological successes, paleobiology has lagged behind, due in part to perceived challenges in collecting and analyzing morphological data. As a result, the earlier synthetic evolutionary view developed between neo- and paleontology has not kept pace with the current data-centric landscape. To address these issues, I aim to integrate morphological data representing fossil and living taxa into the modern evolutionary framework through the development of novel statistical approaches that leverage sources of data previously thought to be unconventional. These developments follow two main threads: 1) development of a statistical framework through which to infer phylogeny among fossil taxa by merging increasingly large and high-throughput quantitative morphological datasets with stratigraphic information, and 2) developing empirical applications of new approaches to comprehensively examine long-hypothesized but under-studied patterns in evolutionary rate throughout time, and mosaic change by integrating morphological, stratigraphic, and developmental data.PHDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/149804/1/cfukuchi_1.pd