Timothy M. Collins

Evolutionary history of Northern Hemisphere Nucella (Gastropoda, Muricidae) : Molecular, morphological, ecological, and paleontological evidence

By combining data from a variety of sources we explore patterns of evolution and speciation in Nucella, a widely studied genus of shallow‐water marine neogastropods. We present a hypothesis of phylogenetic relationships for all of the currently recognized species of northern hemisphere Nucella, based on an analysis of 718 base pairs of nucleotide sequence from the mitochondrial cytochrome b gene. The order of appearance of species in the fossil record is congruent with this hypothesis. The topology of the inferred phylogeny of Nucella, coupled with ecological, morphological, and fossil evidence, was used to address three main questions: (1) At what time and by which route was the North Atlantic invaded from the North Pacific compared to prior studies of the trans‐Arctic interchange? (2) Do patterns of molecular variation within species corroborate the importance of climatic cycles in driving speciation in north temperate marine animals? (3) Was radiation in the direction of increased or decreased ecological specialization, body size, or vulnerability to predation?

Developing model systems for molecular biogeography: Vicariance and interchange in marine invertebrates

Inference of shared history, based on congruence between the topological structure of cladograms for lineages, and the geographic distributions of lineages is becoming increasingly important to ecological and behavioral evolutionary studies. Yet clades which are topologically and geographically congruent may have originated at very different times, a phenomenon known as “pseudocongruence”. In this chapter, we explore the strengths and weaknesses of molecular data in identifying cases of pseudocongruence for the simplest possible case: when sister taxa are found in neighboring areas now separated by a disjunction or barrier of some kind. We focus on studies of littoral marine invertebrates in three well-studied marine model systems: coastal species from the southeastern United States, species pairs divided by the final closure of the Panama Seaway ca. 3 million years ago, and taxa which took part in the trans-Arctic interchange between the Pacific and Atlantic Oceans following the opening of the Bering Strait ca. 3.5 million years ago. For each of these model systems, we present molecular divergence, population genetic, and in some cases, paleontological evidence that sister taxa in neighboring areas likely diverged at different times. We also show that comparison of multiple data sets from the same taxa can reveal cases of rate variation. While comparisons of degree of molecular divergence may be confounded by rate variation, comparisons of phylogeographic structure also have the potential to distinguish between cases of strong geographical subdivision and recent gene flow.

Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters

Abstract. To re-evaluate the relationships of the major bivalve lineages, we amassed detailed morpho-anatomical, ultrastructural and molecular sequence data for a targeted selection of exemplar bivalves spanning the phylogenetic diversity of the class. We included molecular data for 103 bivalve species (up to five markers) and also analysed a subset of taxa with four additional nuclear protein-encoding genes. Novel as well as historically employed morphological characters were explored, and we systematically disassembled widely used descriptors such as gill and stomach ‘types’. Phylogenetic analyses, conducted using parsimony direct optimisation and probabilistic methods on static alignments (maximum likelihood and Bayesian inference) of the molecular data, both alone and in combination with morphological characters, offer a robust test of bivalve relationships. A calibrated phylogeny also provided insights into the tempo of bivalve evolution. Finally, an analysis of the informativeness of morphological characters showed that sperm ultrastructure characters are among the best morphological features to diagnose bivalve clades, followed by characters of the shell, including its microstructure. Our study found support for monophyly of most broadly recognised higher bivalve taxa, although support was not uniform for Protobranchia. However, monophyly of the bivalves with protobranchiate gills was the best-supported hypothesis with incremental morphological and/or molecular sequence data. Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata and Imparidentia new clade ( = Euheterodonta excluding Anomalodesmata) were recovered across analyses, irrespective of data treatment or analytical framework. Another clade supported by our analyses but not formally recognised in the literature includes Palaeoheterodonta and Archiheterodonta, which emerged under multiple analytical conditions. The origin and diversification of each of these major clades is Cambrian or Ordovician, except for Archiheterodonta, which diverged from Palaeoheterodonta during the Cambrian, but diversified during the Mesozoic. Although the radiation of some lineages was shifted towards the Palaeozoic (Pteriomorphia, Anomalodesmata), or presented a gap between origin and diversification (Archiheterodonta, Unionida), Imparidentia showed steady diversification through the Palaeozoic and Mesozoic. Finally, a classification system with six major monophyletic lineages is proposed to comprise modern Bivalvia: Protobranchia, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and Imparidentia.

Beyond area relationships: Extinction and recolonization in molecular marine biogeography

In vicariance biogeography, the traditional focus on solely determining area relationships can obscure biologically interesting complexity. Even in the case of neighboring sister areas, the rise and fall of barriers to dispersal can yield a complex pattern of vicariance and interchange. Vicariance biogeographers view incongruent historical patterns as noise that must be filtered out. Here, we sharpen the focus of vicariance biogeography, and attempt to identify organismal characteristics that unite sets of taxa with congruent histories. Emphasizing examples from coastal marine invertebrates, we apply this perspective to two well-studied model systems: the southeastern United States, and the trans-Arctic interchange through the Bering Strait.

Changing identities: tRNA duplication and remolding within animal mitochondrial genomes

Although the majority of metazoan mitochondrial genomes (mtDNAs) contain the same 37 genes, including 22 encoding transfer RNAs (tRNAs), the recognition of orthologs is not always straightforward. Here we demonstrate that inferring tRNA orthologs among taxa by using anticodon triplets and deduced secondary structure can be misleading: through a process of tRNA duplication and mutation in the anticodon triplet, remolded leucine (LUUR) tRNA genes have repeatedly taken over the role of isoaccepting LCUN leucine tRNAs within metazoan mtDNA. In the present work, data from within the gastropods and a broad survey of metazoan mtDNA suggest that tRNA leucine duplication and remolding events have occurred independently at least seven times within three major animal lineages. In all cases where the mechanism of gene remolding can be inferred with confidence, the direction is the same: from LUUR to LCUN. Gene remolding and its apparent asymmetry have significant implications for the use of mitochondrial tRNA gene orders as phylogenetic markers. Remolding complicates the identification of orthologs and can result in convergence in gene order. Careful sequence-based analysis of tRNAs can help to recognize this homoplasy, improving gene-order-based phylogenetic hypotheses and underscoring the importance of careful homology assessment. tRNA remolding also provides an additional mechanism by which gene order changes can occur within mtDNA: through the changing identity of tRNA genes themselves. Recognition of these remolding events can lead to new interpretations of gene order changes, as well as the discovery of phylogenetically relevant gene dynamics that are hidden at the level of gene order alone.

Phylogenetic and Ontogenetic Influences on the Distribution of Anthocyanins and Betacyanins in Leaves of Tropical Plants

We examined the anatomy of expanding, mature, and senescing leaves of tropical plants for the presence of red pigments: anthocyanins and betacyanins. We studied 463 species in total, 370 genera, belonging to 94 families. This included 21 species from five families in the Caryophyllales, where betacyanins are the basis for red color. We also included 14 species of ferns and gymnosperms in seven families and 29 species with undersurface coloration at maturity. We analyzed 399 angiosperm species (74 families) for factors (especially developmental and evolutionary) influencing anthocyanin production during expansion and senescence. During expansion, 44.9% produced anthocyanins and only 13.5% during senescence. At both stages, relatively few patterns of tissue distributions developed, primarily in the mesophyll, and very few taxa produced anthocyanins in dermal and ground tissue simultaneously. Of the 35 species producing anthocyanins both in development and senescence, most had similar cellular distributions. Anthocyanin distributions were identical in different developing leaves of three heteroblastic taxa. Phylogeny has influenced the distribution of anthocyanins in the epidermis and mesophyll of expanding leaves and the palisade parenchyma during senescence, although these influences are not strong. Betacyanins appear to have similar distributions in leaves of taxa within the Caryophyllales and, perhaps, similar functions. The presence of anthocyanins in the mesophyll of so many species is inconsistent with the hypothesis of protection against UV damage or fungal pathogens, and the differing tissue distributions indicate that the pigments may function in different ways, as in photoprotection and free‐radical scavenging.

Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics.

The advent of genomics has fueled optimism for improvement in the reliability and accuracy of phylogenetic trees. An implicit assumption is that there will be an inexorable improvement in phylogenetic accuracy as the number of genes used increases, and that this approach is necessary because there are no identifiable parameters that predict the phylogenetic performance of genes (Gee, 2003; Rokas et al. 2003). These issues were explored in the recent article by Rokas et al. who investigated the phylogenetic signal in a sample of 106 protein-encoding genes selected from the genomes of 8 species of yeast. Rokas et al. (2003) analyzed these genes separately, and in combination, showing that individual genes sometimes support conflicting topologies. Although considerable character incongruence existed in the combined data set, simultaneous analysis of all genes resulted in one tree with 100% bootstrap proportions (BP) at all nodes. This “species tree” was taken to represent the true phylogeny (Fig. 1a topology). The authors then carried out a series of analyses with randomly concatenated data sets of varying size to determine the minimum amount of data required to establish confidence in the species tree at a given level of statistical significance. They concluded that a minimum of 20 randomly concatenated genes was required to infer relationships confidently and that “It is only through the analyses of larger amounts of sequence data that confidence in the proposed phylogenetic reconstruction can be obtained” and further “that analyses based on a single or a small number of genes provide insufficient evidence for establishing or refuting phylogenetic relationships.” They also expressed the opinion that the result for these yeast species was likely to be typical for molecular phylogenetic studies: “. . . we believe that this group is a representative model for key issues that researchers in phylogenetics are confronting,” with the clear implication that the majority of current molecular phylogenies must be considered unreliable. Another important conclusion was that there are no predictors of phylogenetic performance of genes: “there were no identifiable parameters that could systematically account for or predict the performance of single genes.” Similarly, Gee (2003), in discussing the Rokas et al. (2003) paper states, “there are no identifiable parameters that can predict the performance of genes in any systematic way.” Finally, they noted that bootstrap values were lower and variance higher for contiguous gene sequences than for randomly sampled orthologous nucleotides and took this as evidence of the misleading signal in individual genes resulting from the nonindependence of nucleotides within genes. These conclusions, if true, are sobering for those attempting to infer relationships using DNA sequences with limited time and budgets. Herein, we demonstrate that these conclusions require substantial revision. First we show that many genes in the yeast data set published by Rokas et al. (2003) have nucleotide frequencies that have shifted markedly among taxa at third positions of codons. These nucleotide sequences deviate significantly from the stationary condition (see also Phillips et al., 2004). Second, we illustrate through a series of analyses that the stationary gene partition is superior to the nonstationary partition, recovering the underlying phylogeny with many fewer genes. Finally, we show that the conclusion of Rokas et al. regarding the superiority of random sampling of orthologous nucleotides relative to contiguous sequences for phylogenetic analysis is largely an artifact of different bootstrap treatments for these two sampling schemes. Rokas et al. (2003) used several criteria for sampling and retaining genes from seven species of Saccharomyces yeasts, and one outgroup species, Candida albicans (Fig. 1). Genes were spaced at approximately 40-kilobase intervals. Only protein-encoding genes with identifiable and generally alignable homologs in all eight

A phylogenetic backbone for Bivalvia: an RNA-seq approach.

Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000–20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals.

Sessile snails, dynamic genomes: gene rearrangements within the mitochondrial genome of a family of caenogastropod molluscs

BackgroundWidespread sampling of vertebrates, which comprise the majority of published animal mitochondrial genomes, has led to the view that mitochondrial gene rearrangements are relatively rare, and that gene orders are typically stable across major taxonomic groups. In contrast, more limited sampling within the Phylum Mollusca has revealed an unusually high number of gene order arrangements. Here we provide evidence that the lability of the molluscan mitochondrial genome extends to the family level by describing extensive gene order changes that have occurred within the Vermetidae, a family of sessile marine gastropods that radiated from a basal caenogastropod stock during the Cenozoic Era.ResultsMajor mitochondrial gene rearrangements have occurred within this family at a scale unexpected for such an evolutionarily young group and unprecedented for any caenogastropod examined to date. We determined the complete mitochondrial genomes of four species (Dendropoma maximum, D. gregarium, Eualetes tulipa, and Thylacodes squamigerus) and the partial mitochondrial genomes of two others (Vermetus erectus and Thylaeodus sp.). Each of the six vermetid gastropods assayed possessed a unique gene order. In addition to the typical mitochondrial genome complement of 37 genes, additional tRNA genes were evident in D. gregarium (trnK) and Thylacodes squamigerus (trnV, trnLUUR ). Three pseudogenes and additional tRNAs found within the genome of Thylacodes squamigerus provide evidence of a past duplication event in this taxon. Likewise, high sequence similarities between isoaccepting leucine tRNAs in Thylacodes, Eualetes, and Thylaeodus suggest that tRNA remolding has been rife within this family. While vermetids exhibit gene arrangements diagnostic of this family, they also share arrangements with littorinimorph caenogastropods, with which they have been linked based on sperm morphology and primary sequence-based phylogenies.ConclusionsWe have uncovered major changes in gene order within a family of caenogastropod molluscs that are indicative of a highly dynamic mitochondrial genome. Studies of mitochondrial genomes at such low taxonomic levels should help to illuminate the dynamics of gene order change, since the telltale vestiges of gene duplication, translocation, and remolding have not yet been erased entirely. Likewise, gene order characters may improve phylogenetic hypotheses at finer taxonomic levels than once anticipated and aid in investigating the conditions under which sequence-based phylogenies lack resolution or prove misleading.

Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca)

Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting morphological and molecular hypotheses. Marked incongruity of phylogenetic signal in datasets heavily represented by nuclear ribosomal genes versus mitochondrial genes has also impeded consensus on the type of molecular data best suited for investigating bivalve relationships. To arbitrate conflicting phylogenetic hypotheses, we evaluated the utility of four nuclear protein-encoding genes-ATP synthase β, elongation factor-1α, myosin heavy chain type II, and RNA polymerase II-for resolving the basal relationships of Bivalvia. We sampled all five major lineages of bivalves (Archiheterodonta, Euheterodonta [including Anomalodesmata], Palaeoheterodonta, Protobranchia, and Pteriomorphia) and inferred relationships using maximum likelihood and Bayesian approaches. To investigate the robustness of the phylogenetic signal embedded in the data, we implemented additional datasets wherein length variability and/or third codon positions were eliminated. Results obtained include (a) the clade (Nuculanida+Opponobranchia), i.e., the traditionally defined Protobranchia; (b) the monophyly of Pteriomorphia; (c) the clade (Archiheterodonta+Palaeoheterodonta); (d) the monophyly of the traditionally defined Euheterodonta (including Anomalodesmata); and (e) the monophyly of Heteroconchia, i.e., (Palaeoheterodonta+Archiheterodonta+Euheterodonta). The stability of the basal tree topology to dataset manipulation is indicative of signal robustness in these four genes. The inferred tree topology corresponds closely to those obtained by datasets dominated by nuclear ribosomal genes (18S rRNA and 28S rRNA), controverting recent taxonomic actions based solely upon mitochondrial gene phylogenies.