Evolution and phylogeny of coccidia with the eimerian-type and isomeric-type oocysts

The isosporan-type of oocysts is a later evolutionary purchase in comparison with the eimerioran-type construction of oocysts'. Identical number of sporocysts and sporozoits in the oocysts, bivalvular constructions of sporocysts, heteroxenous life cycles and endogenous sporulation in a group series of coccidia have arisen asynchronously and independently. The evolution of RNA genes and a type of oocysts construction was proceeded in different species of the isosporan-type coccidia and with different velocities.     

Trachylina: The Group That Remains Enigmatic Despite 150 Years of Investigations

Trachylina is a group of cnidarians, a subclass of Hydrozoa. Despite the low species diversity of this group, its representatives are characterized by diversity of life cycles. Trachylina have populated various environments, from deep ocean to fresh water ecosystems. Polyps of Trachylina are either very small or absent in the life cycle, which distinguishes this group from the majority of other Hydrozoa. Trachylina are also highly diverse and have a number of features that are unusual for cnidarians. A number of representatives of this group are characterized by a small number of cells at the embryonic and larval stages. This phenomenon is well known for the representatives of phylogenetically distant taxa—Nematoda and Chordata (Tunicata). In addition, the development of Trachylina is characterized by a number of evolutionary changes that, apparently, make it possible to accelerate the formation of the definitive stage (medusa). Paradoxically, there is no one species among the representatives of this group that is studied in more or less detail. The purpose of our review is to summarize the scanty information on the Trachylina ontogeny and to demonstrate the importance of studying the ontogeny of this group for understanding the general rules of the evolution of development and life cycles of Metazoa.     

Evolution of dispersal in spatially and temporally variable environments: The importance of life cycles

Spatiotemporal variability of the environment is bound to affect the evolution of dispersal, and yet model predictions strongly differ on this particular effect. Recent studies on the evolution of local adaptation have shown that the life cycle chosen to model the selective effects of spatiotemporal variability of the environment is a critical factor determining evolutionary outcomes. Here, we investigate the effect of the order of events in the life cycle on the evolution of unconditional dispersal in a spatially heterogeneous, temporally varying landscape. Our results show that the occurrence of intermediate singular strategies and disruptive selection are conditioned by the temporal autocorrelation of the environment and by the life cycle. Life cycles with dispersal of adults versus dispersal of juveniles, local versus global density regulation, give radically different evolutionary outcomes that include selection for total philopatry, evolutionary bistability, selection for intermediate stable states, and evolutionary branching points. Our results highlight the importance of accounting for life‐cycle specifics when predicting the effects of the environment on evolutionarily selected trait values, such as dispersal, as well as the need to check the robustness of model conclusions against modifications of the life cycle.     

A framework to compare theoretical predictions on trait evolution in temporally varying environments under different life cycles

Predicting the evolution of traits such as dispersal or local adaptation, in a variable environment is an important issue in theoretical evolutionary ecology. With concepts such as hard selection vs. soft selection or fine-grained vs. coarse-grained environmental variability, this issue has attracted much attention, and yet different models seldom agree on qualitative predictions about, e.g. the evolution of generalist or specialist strategies, or the occurrence of stabilizing or disruptive selection on studied traits.Here, I investigate the effect of the order of events in the life cycle on trait evolution in a spatially heterogeneous, temporally varying landscape using a Wright–Fisher island model. I first develop a methodological framework allowing for different life cycles. Then I illustrate the importance of life cycles on selection regimes by looking more closely at the evolution of local adaptation.Model results show that the occurrence of disruptive selection and bi- or tristability mainly depends on the life cycle, the convexity of the trade-off behind local adaptation, the immigration rate, and the autocorrelation in patch state. With the same forces driving the evolution of local adaptation, different life cycles induce different evolutionary outcomes. Model results highlight the importance of accounting for life cycle specificities when attempting to predict the effects of the environment on evolutionarily selected trait values, as well as the need to check the robustness of evolutionary model conclusions against modifications of the life cycle.     

The Challenge of Fish Coccidia1

Species of Eimeria occurring in fishes show important differences, especially in their life cycles, with respect to what is known for those forms found in mammals or other hosts. In some cases, at least, some small invertebrate may play the role of vector or intermediate host. Present studies of fish coccidia may throw light on the possible evolution of certain aspects of host-parasite interrelationships involving eimerian species in particular: for example, the earliest site (perhaps not the gut) of infection and even the “original” host group (perhaps invertebrates rather than vertebrates).     

Evolution of multihost parasites

Multihost parasites can infect different types of hosts or even different host species. Epidemiological models have shown the importance of the diversity of potential hosts for understanding the dynamics of infectious disease (e.g., the importance of reservoirs), but the consequences of this diversity for virulence and transmission evolution remain largely overlooked. Here, I present a general theoretical framework for the study of life-history evolution of multihost parasites. This analysis highlights the importance of epidemiology (the relative quality and quantity of different types of infected hosts) and between-trait constraints (both within and between different hosts) to parasite evolution. I illustrate these effects in different transmission scenarios under the simplifying assumption that parasites can infect only two types of hosts. These simple but contrasted evolutionary scenarios yield new insights into virulence evolution and the evolution of transmission routes among different hosts. Because many of the pathogens that have large public-health and agricultural impacts have complex life cycles, an understanding of their evolutionary dynamics could hold substantial benefits for management.     

The current status of the small subunit rRNA phylogeny of the coccidia (Sporozoa)

There is no current comprehensive assessment of the molecular phylogeny of the coccidia, as all recently published papers either deal with subsets of the taxa or sequence data, or provide non-robust analyses. Here, we present a comprehensive and consistent phylogenetic analysis of the available data for the small-subunit ribosomal RNA gene sequence, including a number of taxa not previously studied, based on a Bayesian tree-building analysis and the covariotide model of evolution. The assumptions of the analysis have been rigorously tested, and the benefits and limitations highlighted. Our results provide support for a number of prior conclusions, including the monophyly of the families Sarcocystidae (cyst-forming coccidia) and Eimeriidae (oocyst-forming coccidia), but with bird-host Isospora species in the Eimeriidae and mammal-host species in the Sarcocystidae. However, it is clear that a number of previously reported relationships are dependent on the evolutionary model chosen, such as the placements of Goussia janae, Lankesterella minimia and Caryospora bigenetica. Our results also confirm the monophyly of the subfamilies Toxoplasmatinae and Sarcocystinae, but only some of the previously reported groups within these subfamilies are supported by our analysis. Similarly, only some of the previously reported groups within the Eimeriidae are supported by our analysis, and the genus Eimeria is clearly paraphyletic. There are unambiguous patterns of host-parasite relationship within the coccidia, as most of the well-supported groups have a consistent and restricted range of hosts, with the exception of the Toxoplasmatinae. Furthermore, the previously reported groups for which we found no support all have a diverse range of unrelated hosts, confirming that these are unlikely to be natural groups. The most interesting unaddressed questions may relate to Isospora, which has the fewest available sequences and host-parasite relationships apparently not as straightforward as elsewhere within the suborder.     

Variation and evolution of the complex life cycle in Adelgidae (Hemiptera)

The family Adelgidae is a small group of insects within Aphidoidea (Hemiptera). Adelgids are typically holocyclic with host‐alternation between the primary and secondary hosts, but some anholocyclic species persist either on the primary or secondary host. Like Aphididae, complexities and variation of adelgid life cycles are good models for understanding the evolution of complex life cycles. In this review, we outline the complex life cycles of adelgids, and current status and recent advances in adelgid life cycle studies. We also discuss the evolution of adelgid life cycles by comparing them to closely related aphid life cycles. A switch from holocycly to anholocycly on the primary host needs evolutionary innovations in gallicola behavior and reproduction. This radical evolution can be explained by mutations in a regulatory system that controls the sequence of gene sets producing phenotypes of one morph. In contrast, anholocycly on the secondary host consists of a series of exulis generations already existing in the holocycle. Thus, it may evolve by loss of primary‐host generations through extinction of the primary host, expansion beyond the geographical range of the primary host, or loss of male‐producing sexuparae that return to the primary host. Although the holocycle and its anholocyclic derivatives have been regarded as different species, morphological, ecological and genetic differences are too subtle to separate them into different species. The holocycle and its anholocyclic derivatives should not be split into different species without clearly identifiable morphological differences.     

Ecological and evolutionary consequences of linked life-history stages in the sea

Naturalists and scientists have been captivated by the diversity of marine larval forms since they were discovered following the advent of the microscope. Because they often bear little resemblance to adults, larvae were identified initially as new life forms, classified into different groups based on the similarity of their body plans and given new names that are still with us today. The radically different body plans and lifestyles of marine larvae and adults have led most investigators historically to study the two phases of complex life cycles in isolation. More recently, important ecological insights have sprung from taking a holistic view of marine life cycles. Meanwhile, the evolutionary (phenotypic and genetic) links among life-history phases remain less appreciated. In this review, our objective is to evaluate the evolutionary links within marine life cycles, and explore their ecological and evolutionary consequences. We provide a brief overview of marine life histories, discuss the phenotypic and genetic links between the two phases of the life cycle and pose challenges to advance our understanding of the evolutionary constraints acting on marine life histories.     

The conceptual basis for a new classification of the coccidia

At the joint meeting of the 8th International Coccidiosis Conference and the Annual Scientific Meeting of the Australian Society for Parasitology in Palm Cove, Australia, in July 2001, a Controversial Roundtable was held on 'New classification of coccidia'. The aim of this Roundtable was to stimulate and encourage discussion and debate on current classification schemes for the group of parasitic protozoa known as the eimeriid coccidia. In the past, such classifications have been based only on phenotypic characters such as morphology, ultrastructure, life cycles, and host specificity. However, over the past 10-15 years, molecular phylogenetic studies on taxa of the eimeriid coccidia have revealed that several of the families, subfamilies, and genera that have been erected based on non-molecular characters are paraphyletic. Therefore, this Roundtable was an important forum for initial discussions on how a new and more comprehensive classification of the eimeriid coccidia, which takes into consideration both phenotypic and molecular characters, can be devised. The stimulus came from invited speakers who gave introductions into selected areas of taxonomy and classification. Following these introductions, a more general discussion with the audience addressed potential steps that may be taken in future work. This review is the immediate outcome of the Roundtable. It describes advantages and disadvantages of the use of phenotypic or molecular characters as the base for taxonomic schemes for eimeriid coccidia. It gives specific examples for drawbacks of current classifications based only on phenotypic characters as well as potential pitfalls associated with the use of only molecular phylogenies. It addresses current controversies as well as rules of taxonomy and nomenclature relevant for the eimeriid coccidia. Finally, it recommends the establishment of an international group of scientists to meet on a regular basis, stimulate further discussions, and give direction on how the final goal, i.e. a proposal for a revised, and widely accepted, classification of the eimeriid coccidia, may be achieved.     

The major parasitic platyhelminth classes — progressive or regressive evolution?

The evolution of certain ontogenetic processes appears to be of special importance to subsequent evolution of a phyletic line, and their occurrence suggests there are various evolutionary capacity levels occupied by major taxa. Two groups that are at the same evolutionary capacity level probably originated in common within that level, which in turn is often shared with several other groups. Morphogenesis by invagination is characteristic of an early evolutionary capacity level common to poriferans, cnidarians, deuterostomes, and platyhelminths, inter alia. In the early ontogeny of the former three groups, this process produces the blastopore and archenteron, but in platyhelminths, e.g. rhabdocoels, two different processes form the digestive system: the mouth forms by invagination and the intestine by a split in the mesenchyme/parenchyma. I have selected some characters and processes to illustrate evolutionary capacity levels and to describe the possible origin of a number of invertebrate groups from various levels and their inter-relationships. My analysis on the basis of evolutionary capacity levels suggests that the deuterostomes originated early (very likely before mollusks and annelids), that tegumental absorption of nutriments is the original mode of nutriment uptake and so predates intestinal ingestion in Platyhelminthes, that ontogenetic characters show that the presumed origin of cercomeromorphaeans from rhabdocoels is improbable, and that features of ontogeny and life cycles indicate that the major parasitic platyhelminth classes arose through progressive rather than regressive evolution. Thus the non-parasitic and the parasitic platyhelminth classes very likely belong to separate evolutionary lines, all originating from the same evolutionary capacity level.     

Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes

BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary mechanism among prokaryotes. The situation in eukaryotes is less clear; the human genome sequence failed to give strong support for any recent transfers from prokaryotes to vertebrates, yet a number of LGTs from prokaryotes to protists (unicellular eukaryotes) have been documented. Here, we perform a systematic analysis to investigate the impact of LGT on the evolution of diplomonads, a group of anaerobic protists.RESULTS: Phylogenetic analyses of 15 genes present in the genome of the Atlantic Salmon parasite Spironucleus barkhanus and/or the intestinal parasite Giardia lamblia show that most of these genes originated via LGT. Half of the genes are putatively involved in processes related to an anaerobic lifestyle, and this finding suggests that a common ancestor, which most probably was aerobic, of Spironucleus and Giardia adapted to an anaerobic environment in part by acquiring genes via LGT from prokaryotes. The sources of the transferred diplomonad genes are found among all three domains of life, including other eukaryotes. Many of the phylogenetic reconstructions show eukaryotes emerging in several distinct regions of the tree, strongly suggesting that LGT not only involved diplomonads, but also involved other eukaryotic groups.CONCLUSIONS: Our study shows that LGT is a significant evolutionary mechanism among diplomonads in particular and protists in general. These findings provide insights into the evolution of biochemical pathways in early eukaryote evolution and have important implications for studies of eukaryotic genome evolution and organismal relationships. Furthermore, "fusion" hypotheses for the origin of eukaryotes need to be rigorously reexamined in the light of these results.     

Ontogenetic systematics: The synthesis of taxonomy, phylogenetics, and evolutionary developmental biology

The main purpose of the present review is to draw attention to growing problems in the modern systematics and phylogenetics which are presently underestimated by the professional community. The dramatic reduction of the importance of ontogeny and morphology in phylogenetic studies of the second part of the 20th century is considered among the major factors of the modern taxonomic and evolutionary paradigm. The deep contradiction of modern approaches, which either merely consider systematics and phylogeny as genealogy or even in a neotypolgical manner irrespective of the evolutionary idea, is demonstrated. Thus, despite the widespread opinion that the evolutionary theory is the major basis for taxonomy, the processes, which in fact caused the origin and formation of the systematic hierarchy are often considered as redundant for the procedure of classification. In this respect, the classical, but well forgotten statement that evolution is a modification of ontogeny is specially highlighted. Tight relationships between evolution, ontogeny, systematics, and phylogenetics are prima facie obvious, but also presently underestimated, although the field of the evo-devo is continuously growing. Paradoxically, even despite the outburst of various molecular ontogenetic approaches, the commonly accepted evolutionary paradigm still lacks a general theory for changes in the shape of organisms. As a step towards the development of such a theory, a synthesis (or more exactly, resynthesis) of still largely independently developing major biological fields, i.e., ontogenetic and evolutionary studies, on the one hand, and traditional taxonomy, on the other hand, a new concept of ontogenetic systematics is proposed. The new concept is intended for integration of supposedly ??immobile?? traditional taxonomy with the dynamics, but predominantly considered as hypothetical, evolutionary field based on the process of ontogeny, which, in contrast to the evolution itself, can be observed in the real time. Therefore, it is concluded that, for instance, the evolution of the main group of living organisms Metazoa, is primarily the evolution of a very limited number of ontogenetic cycles that were formed as early as the Early Cambrian. A significant underestimation of cyclic properties of ontogeny in the evolution and systematics is shown. Using two model groups, echinoderms of the class Ophiuroidea and dorid nudibranch mollusks (Gastropoda: Doridacea), practical importance of the integrative approach developed here is demonstrated. The ??disruption?? of the ancestral ontogenetic cycle and further formation of a new descendant cycle (which implies some continuity of ancestral and descendant characters) is considered to be a major evolutionary pattern. The model proposed implies either progressive (addition of stages and characters) or regressive (reduction of already existing stages and structures) modification of ancestral taxon, the diagnosis of which corresponds to the model of its ontogenetic cycle. In the extreme cases of disruption of the ancestral ontogenetic cycle, adult characters of descendants are substituted by juvenile ancestral features, demonstrating paedomorphoses in the narrow sense. Within the framework of the approach proposed, the evolutionary and ontogenetic models of ancestral ontogenetic cycles of brittle stars and dorid nudibranchs are developed and discussed. Based on the original material of the extinct Paleozoic ophiuroid group Oegophiurida, the origin of key evolutionary novelties is discussed. A major conclusion of the present review is the high necessity of integration of new molecular data with already well-established taxonomic hierarchy and ontogenetic information as a basis for the development of the general theory of transformations of organisms, i.e., the theory of evolution in its true sense.     

Evolutionary relationships among cyst-forming coccidia Sarcocystis spp. (Alveolata: Apicomplexa: Coccidea) in endemic African tree vipers and perspective for evolution of heteroxenous life cycle

Cyst-forming coccidia of the genus Sarcocystis (Alveolata: Apicomplexa: Coccidea) parasitize vertebrates worldwide. Data from the small subunit rRNA genes (SSU) and the D2 domain of the large subunit rRNA genes were used to reconstruct phylogeny for all species in the Sarcocystidae for which sequences are currently available. We have focused on the evolutionary history of species that circulate between snakes as definitive hosts and rodents as intermediate hosts. Trees were reconstructed using maximum parsimony, minimum evolution, maximum likelihood and the bayesian phylogenetics. Our reconstructions support monophyly of Sarcocystidae but fail to robustly resolve the relationship within clades. Using a concatenated dataset of available rDNAs, the "isosporoid" coccidia Neospora, Toxoplasma, Besnoitia, Isospora and Hyaloklossia form a sister group to the monophyletic Sarcocystis. Moreover, we show that Sarcocystis from arboreal vipers of the genus Atheris, which are endemic to the mountain rain forests of the Equatorial Africa, are monophyletic, with sister species parasitizing the desert viper Pseudocerastes persicus from the Near East. We report the co-evolution of Sarcocystis spp. with their final snake hosts. The geological history of the African continent, mountain ranges, forests and general SSU rDNA rates were used to construct a linearized tree. Possible origin of the heteroxenous life cycle of Sarcocystis is discussed.     

Experimental evolution of multicellularity using microbial pseudo-organisms

In a major evolutionary transition to a new level of organization, internal conflicts must be controlled before the transition can truly be successful. One such transition is that from single cells to multicellularity. Conflicts among cells in multicellular organisms can be greatly reduced if they consist of genetically identical clones. However, mutations to cheaters that experience one round of within-individual selection could still be a problem, particularly for certain life cycles. We propose an experimental evolution method to investigate this issue, using micro-organisms to construct multicellular pseudo-organisms, which can be evolved under different artificial life cycles. These experiments can be used to test the importance of various life cycle features in maintaining cooperation. They include structured reproduction, in which small propagule size reduces within-individual genetic variation. They also include structured growth, which increases local relatedness within individual bodies. Our method provides a novel way to test how different life cycles favour cooperation, even for life cycles that do not exist.     

THE EVOLUTIONARY IMPLICATIONS OF CONFLICT BETWEEN PARASITES WITH DIFFERENT TRANSMISSION MODES

Understanding the processes that shape the evolution of parasites is a key challenge for evolutionary biology. It is well understood that different parasites may often infect the same host and that this may have important implications to the evolutionary behavior. Here we examine the evolutionary implications of the conflict that arises when two parasite species, one vertically transmitted and the other horizontally transmitted, infect the same host. We show that the presence of a vertically transmitted parasite (VTP) often leads to the evolution of higher virulence in horizontally transmitted parasites (HTPs), particularly if the VTPs are feminizing. The high virulence in some HTPs may therefore result from coinfection with cryptic VTPs. The impact of an HTP on a VTP evolution depends crucially on the nature of the life‐history trade‐offs. Fast virulent HTPs select for intermediate feminization and virulence in VTPs. Coevolutionary models show similar insights, but emphasize the importance of host life span to the outcome, with higher virulence in both types of parasite in short‐lived hosts. Overall, our models emphasize the interplay of host and parasite characteristics in the evolutionary outcome and point the way for further empirical study.     

Mathematics,genetics and evolution

The importance of mathematics and statistics in genetics is well known. Perhaps less well known is the importance of these subjects in evolution. The main problem that Darwin saw in his theory of evolution by natural selection was solved by some simple mathematics. It is also not a coincidence that the re-writing of the Darwinian theory in Mendelian terms was carried largely by mathematical methods. In this article I discuss these historical matters and then consider more recent work showing how mathematical and statistical methods have been central to current genetical and evolutionary research.     

Symbiosis versus competition in plant virus evolution

Darwin's theory of evolution by natural selection has been supported by molecular evidence and by experimental evolution of viruses. However, it might not account for the evolution of all life, and an alternative model of evolution through symbiotic relationships also has gained support. In this review, the evolution of plant viruses has been reinterpreted in light of these two seemingly opposing theories by using evidence from the earliest days of plant virology to the present. Both models of evolution probably apply in different circumstances, but evolution by symbiotic association (symbiogenesis) is the most likely model for many evolutionary events that have resulted in rapid changes or the formation of new species. In viruses, symbiogenesis results in genomic reassortment or recombination events among disparate species. These are most noticeable by phylogenetic comparisons of extant viruses from different taxonomic groups.     

Evolution of spatially structured host–parasite interactions

Spatial structure has dramatic effects on the demography and the evolution of species. A large variety of theoretical models have attempted to understand how local dispersal may shape the coevolution of interacting species such as host–parasite interactions. The lack of a unifying framework is a serious impediment for anyone willing to understand current theory. Here, we review previous theoretical studies in the light of a single epidemiological model that allows us to explore the effects of both host and parasite migration rates on the evolution and coevolution of various life‐history traits. We discuss the impact of local dispersal on parasite virulence, various host defence strategies and local adaptation. Our analysis shows that evolutionary and coevolutionary outcomes crucially depend on the details of the host–parasite life cycle and on which life‐history trait is involved in the interaction. We also discuss experimental studies that support the effects of spatial structure on the evolution of host–parasite interactions. This review highlights major similarities between some theoretical results, but it also reveals an important gap between evolutionary and coevolutionary models. We discuss possible ways to bridge this gap within a more unified framework that would reconcile spatial epidemiology, evolution and coevolution.     

Shedding new light on opsin evolution

Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function.