Patricia Dyal

Multiple Origins of Anaerobic Ciliates with Hydrogenosomes within the Radiation of Aerobic Ciliates

Some ciliates live anaerobically and lack mitochondria, but possess hydrogenosomes: organelles that contain hydrogenase and produce hydrogen. The origin of hydrogenosomes has been explained by two competing hypotheses: (i) they are biochemically modified mitochondria; or (ii) they are derived from endosymbiotic association(s) of ciliates and anaerobic eubacteria that possessed the hydrogenosome biochemistry. Phylogenetic analyses of representative aerobic, and anaerobic hydrogenosomal ciliates using host nuclear SSU rDNA sequences indicate a minimum of three, but more likely four, separate origins of hydrogenosomes. Whereas this does not refute either hypothesis, the implausibility of multiple convergent endosymbioses gives further support to the view that hydrogenosomes in ciliates derive from an existing organelle, which ultrastructural evidence suggests is the mitochondrion. Our results indicate a considerable potential for physiological-biochemical plasticity among a group of predominantly aerobic eucaryotes, and provide a phylogenetic framework to further refine and test hypotheses of the origins of the hydrogenosomal enzymes.

Hydrogenosomes, Mitochondria and Early Eukaryotic Evolution

Available data suggest that unusual organelles called hydrogenosomes, that make ATP and hydrogen, and which are found in diverse anaerobic eukaryotes, were once mitochondria. The evolutionary origins of the enzymes used to make hydrogen, pyruvate:ferredoxin oxidoreductase (PFO) and hydrogenase, are unresolved, but it seems likely that both were present at an early stage of eukaryotic evolution. Once thought to be restricted to a few unusual anaerobes, these proteins are found in diverse eukaryotic cells, including our own, where they are targeted to different cell compartments. Organelles related to mitochondria and hydrogenosomes have now been found in species of anaerobic and parasitic protozoa that were previously thought to have separated from other eukaryotes before the mitochondrial endosymbiosis. Thus it is possible that all eukaryotes may eventually be shown to contain an organelle of mitochondrial ancestry, bearing testimony to the important role that the mitochondrial endosymbiosis has played in eukaryotic evolution. It remains to be seen if members of this family of organelles share a common function essential to the eukaryotic cell, that provides the underlying selection pressure for organelle retention under different living conditions.

Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin for both organelles

Mitochondria are one of the hallmarks of eukaryotic cells, exporting ATP in exchange for cytosolic ADP using ADP/ATP carriers (AAC) located in the inner mitochondrial membrane. In contrast, several evolutionarily important anaerobic eukaryotes lack mitochondria but contain hydrogenosomes, peculiar organelles of controversial ancestry that also supply ATP but, like some fermentative bacteria, make molecular hydrogen in the process. We have now identified genes from two species of the hydrogenosome‐containing fungus Neocallimastix that have three‐fold sequence repeats and signature motifs that, along with phylogenetic analysis, identify them as AACs. When expressed in a mitochondrial AAC‐ deficient yeast strain, the hydrogenosomal protein was correctly targeted to the yeast mitochondria inner membrane and yielded mitochondria able to perform ADP/ATP exchange. Characteristic inhibitors of mitochondrial AACs blocked adenine nucleotide exchange by the Neocallimastix protein. Thus, our data demonstrate that fungal hydrogenosomes and yeast mitochondria use the same pathway for ADP/ATP exchange. These experiments provide some of the strongest evidence yet that yeast mitochondria and Neocallimastix hydrogenosomes are but two manifestations of the same fundamental organelle.

A molecular phylogeny of heterodont bivalves (Mollusca: Bivalvia: Heterodonta): new analyses of 18S and 28S rRNA genes

A new molecular phylogeny is presented for the highly diverse, bivalve molluscan subclass Heterodonta. The study, the most comprehensive for heterodonts to date, used new sequences of 18S and 28S rRNA genes for 103 species from 49 family groups with species of Palaeoheterodonta (Trigoniidae, Margaritiferidae and Unionidae) as outgroups. Results confirm previous analyses that the Carditidae/Astartidae/Crassatellidae clade is basal to all other heterodonts including Anomalodesmata (often classified as a separate subclass or order). Thyasiroidea occupy a near basal position between the Crassatelloidea and Anomalodesmata. Lucinidae form a well‐supported monophyletic group distinct from Thyasiridae and Ungulinidae. The Solenoidea and Hiatelloidea link as sister groups distant from the Tellinoidea and Myoidea, respectively, where they had been previously associated. The position of the Gastrochaenidae is unstable but does not group with myoidean taxa. Species of four families of Galeommatoidea form a clade that also includes Sportellidae of the Cyamioidea. The Cardioidea and Tellinoidea form highly supported, long branched, individual clades but group as sister taxa. A major clade including Veneroidea, Mactroidea, Myoidea and other families is given the unranked name Neoheterodontei. There is no support for a separate order Myoida (Myoidea and Pholadoidea). Dreissenidae group within the clade including Myidae, Corbulidae, Pholadidae and Teredinidae. The Corbiculoidea is confirmed as polyphyletic with the Sphaeriidae and Corbiculidae forming separate clades within the Neoheterodontei; Corbiculidae grouping with the Glauconomidae. Hemidonacidae are unrelated to the Cardiidae, as previously proposed, but nest within the Neoheterodontei. The Gaimardiidae group near to the Ungulinidae and not with Cyamioidea where most recently classified. The family Ungulinidae, previously classified in the Lucinoidea, forms a well‐supported clade within the Neoheterodontei and is elevated to superfamily rank — Ungulinoidea. The monophyletic status of Glossoidea, Arcticoidea and Veneroidea is unconfirmed. A brief review of the fossil record of the heterodonts indicates that the basal clades of Crassatelloidea, Anomalodesmata and Lucinoidea diverged very early in the Lower Palaeozoic. Other groups such as the Hiatelloidea, Solenoidea, Gastrochaenidae probably were of late Palaeozoic origins. The Cardioidea and Tellinoidea originated in the Triassic while major groups of Neoheterodontei radiated in the Late Mesozoic. The phylogenetic position of the Thyasiroidea and Galeommatoidea suggests a longer fossil history than has so far been recognized.

The phylogeny of the Lepocreadioidea (Platyhelminthes, Digenea) inferred from nuclear and mitochondrial genes: Implications for their systematics and evolution

The phylogenetic relationships of representative species of the superfamily Lepocreadioidea were assessed using partial lsrDNA and nad1 sequences. Forty-two members of the family Lepocreadiidae, six putative members of the Enenteridae, six gyliauchenid species and one Gorgocephalidae, were studied along with 22 species representing 8 families. The Lepocreadioidea is found to be monophyletic, except for the two species of the putative enenterid genus Cadenatella, which are found to be only distantly related to the lepocreadioids. The Lepocreadioidea is formed of five clades in a polytomy, the Gorgocephalidae, a clade containing the Enenteridae and Gyliauchenidae, a small clade of atypical lepocreadiines and the deep-sea lepidapedine lepocreadiids, a small clade consisting of a freshwater form and a group of shallow-water putative lepidapedines and the final clade includes the remaining lepocreadiids. Thus, the generally accepted concept of the Lepocreadiidae is polyphyletic. The Enenteridae (minus Cadenatella) and the Gyliauchenidae are jointly and individually monophyletic, and are sister groups. The nad1 gene on its own places a deep-sea lepocreadiine with the deep-sea lepidapedines, whereas lsrDNA, combined sequences and morphology place this deep-sea lepocreadiine within a group of typical lepocreadiids. It could not be demonstrated that a significant proportion of sites in the nad1 gene evolved under positive selection; this anomalous relationship therefore remains unexplained. Most deep-sea species are in a monophyletic group, a few of which also occur in shallow waters, retaining some characters of the deep-sea clade. Many lepocreadioid species infect herbivorous fish, and it may be that the recently discovered life-cycle involving a bivalve first intermediate host and metacercariae encysted on vegetation is a common life-cycle pattern. The host relationships show no indication of co-speciation, although the host-spectrums exhibited are not random, with related worms tending to utilize related hosts. There are, however, many exceptions. Morphology is found to be of limited value in indicating higher level relationships. For example, even with the benefit of hindsight the gyliauchenids show little morphological similarity to their sister group, the Enenteridae.

Global diversification of mangrove fauna: a molecular phylogeny of Littoraria (Gastropoda: Littorinidae).

The genus Littoraria is one of very few molluscan groups that are closely associated with mangroves. We document its global evolutionary radiation and compare biogeographic patterns with those of mangrove plants, based on phylogenetic and fossil evidence. Using sequences from three genes (nuclear 28S rRNA, mitochondrial 12S rRNA and COI) we reconstruct a phylogeny of 37 of the 39 living morphospecies. Six monophyletic subgenera are defined (Bulimilittorina, Lamellilitorina, Littoraria, Palustorina, Protolittoraria, Littorinopsis) and we synonymize L. coccinea and L. glabrata. A deep division between Palustorina from the Indo-West Pacific and Littoraria from the Atlantic and Eastern Pacific is estimated by a Bayesian relaxed-clock method to be of Middle Eocene to Palaeocene age (43.2-62.7 Ma), which far predates the Early Miocene (18 Ma) closure of the Tethyan Seaway; this, as in mangrove plants, may reflect vicariance by climatic cooling, rather than tectonic processes. The age of Littoraria angulifera in the Atlantic is, however, consistent with Early Miocene vicariance of a Tethyan ancestor. We infer that speciation events are mainly of Miocene or older age, and that diversification has not been driven by depletion of mangrove habitats during recent glacial intervals. Parsimonious reconstruction of ancestral habitats suggests that the genus has inhabited mangrove or wood substrates since its origin, while the rock-dwelling habit of the four members of Protolittoraria is derived. Three species span the Eastern Pacific Barrier, and one is amphi-Atlantic, consistent with a long larval phase of up to 10 weeks. Allopatric speciation is inferred, but usually with subsequent range overlap. Ovoviviparity (interpreted as an adaptation to life in mangroves) has arisen twice.

A global molecular phylogeny of 147 periwinkle species (Gastropoda, Littorininae)

Reid, D. G., Dyal, P. & Williams, S.T. (2012) A global molecular phylogeny of 147 periwinkle species (Gastropoda, Littorininae). —Zoologica Scripta, 41, 125–136.

Cenozoic climate change and diversification on the continental shelf and slope: evolution of gastropod diversity in the family Solariellidae (Trochoidea).

Recent expeditions have revealed high levels of biodiversity in the tropical deep-sea, yet little is known about the age or origin of this biodiversity, and large-scale molecular studies are still few in number. In this study, we had access to the largest number of solariellid gastropods ever collected for molecular studies, including many rare and unusual taxa. We used a Bayesian chronogram of these deep-sea gastropods (1) to test the hypothesis that deep-water communities arose onshore, (2) to determine whether Antarctica acted as a source of diversity for deep-water communities elsewhere and (3) to determine how factors like global climate change have affected evolution on the continental slope. We show that although fossil data suggest that solariellid gastropods likely arose in a shallow, tropical environment, interpretation of the molecular data is equivocal with respect to the origin of the group. On the other hand, the molecular data clearly show that Antarctic species sampled represent a recent invasion, rather than a relictual ancestral lineage. We also show that an abrupt period of global warming during the Palaeocene Eocene Thermal Maximum (PETM) leaves no molecular record of change in diversification rate in solariellids and that the group radiated before the PETM. Conversely, there is a substantial, although not significant increase in the rate of diversification of a major clade approximately 33.7 Mya, coinciding with a period of global cooling at the Eocene–Oligocene transition. Increased nutrients made available by contemporaneous changes to erosion, ocean circulation, tectonic events and upwelling may explain increased diversification, suggesting that food availability may have been a factor limiting exploitation of deep-sea habitats. Tectonic events that shaped diversification in reef-associated taxa and deep-water squat lobsters in central Indo-West Pacific were also probably important in the evolution of solariellids during the Oligo-Miocene.

A molecular perspective on ecological differentiation and biogeography of cyclotrichiid ciliates.

ABSTRACT. Cyclotrichiids are of ecological and evolutionary interest by virtue of their importance in red tide formation, their highly divergent small subunit (SSU) ribosomal RNA (rRNA) genes, kleptoplastidy, and utility as indicators of eutrophication. However, only seven strains have had their SSU rRNA genes sequenced and their environmental diversity and distribution are largely unknown. We probed 67 globally dispersed freshwater column/sediment and soil DNA samples (eDNAs) and constructed 24 environmental gene libraries using polymerase chain reaction primers specific to an uncharacterised cyclotrichiid subgroup. We reveal a novel, globally ubiquitous freshwater clade comprising 25 genetically distinct SSU ribosomal DNA (rDNA) sequences (SSU‐types). Some identical SSU‐types were detected at globally widely distributed sites. The SSU‐types form four distinct phylogenetic clusters according to marine or non‐marine provenance, suggesting at least one major marine–freshwater evolutionary transition within the cyclotrichiids. We used the same primers to sample intensively 18 sampling points in 13 closely situated lakes, each characterised by 14 environmental variables, and showed that molecular detection or non‐detection of cyclotrichiids was most significantly influenced by levels of total phosphorus, dissolved organic carbon, and chlorophyll a. Within the subset of lakes in which cyclotrichiids were detected, closely related SSU‐types differed in their ecological preferences to pH, total phosphorus, and sample depth.

Morphology, ultrastructure, and small subunit rDNA phylogeny of the marine heterotrophic flagellate Goniomonas aff. amphinema.

ABSTRACT. Marine goniomonads have a worldwide distribution but ultrastructural information has not been available so far. An isolate of the heterotrophic marine nanoflagellate Goniomonas (G. aff. amphinema) from North Wales (UK) has been studied, providing information on its morphology and cellular structure using video, electron, laser scanning confocal microscopy (LSCM), and atomic force microscopy. Here, we describe a new feature, a granular area, potentially involved in particle capture and feeding. The binding of the lectin wheat germ agglutinin to the granular area of cells with discharged ejectisomes indicates the adhesive nature of this novel feature. The presence of a microtubular intracellular cytopharynx, apparently also used for feeding, has been revealed by LSCM. The small subunit rRNA gene of the isolate has been sequenced (1,788 bp). Phylogenetic results corroborate significant genetic divergence within the marine members of Goniomonas. This work highlights the need for integrated morphological, ultrastructural, and molecular investigation when describing and studying heterotrophic nanoflagellates.