Molecular phylogeny of the other tissue coccidia: Lankesterella and Caryospora

Nearly complete sequences were obtained from the 18S rDNA genes of Eimeria falciformis (the type species of the genus), Caryospora bigenetica, and Lankesterella minima. Two clones of the rDNA gene from C. higenetica varied slightly in primary structure. Parsimony-based and maximum likelihood phylogenetic reconstructions with a number of other apicomplexan taxa support 2 major clades within the Eucoccidiorida, i.e., the isosporoid coccidia (consisting of Toxoplasma, Neospora, Isospora [in part], and Sarcocystis spp.) and a second clade containing Lankesterella and Caryospora spp., as well as the eimeriid coccidia (Cyclospora, Isospora [in part], and Eimeria spp.). Our observations suggest that Caryospora spp. may not belong in the family Eimeriidae but rather may be allied with the family Lankesterellidae with which they share molecular and life history similarities. This may be a third lineage of coccidian parasites that has independently evolved a unique heteroxenous transmission strategy.     

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.     

Evolution and phylogeny of insect endogenous retroviruses

Background  

The genome of invertebrates is rich in retroelements which are structurally reminiscent of the retroviruses of vertebrates. Those containing three open reading frames (ORFs), including an env -like gene, may well be considered as endogenous retroviruses. Further support to this similarity has been provided by the ability of the env -like gene of DmeGypV (the Gypsy endogenous retrovirus of Drosophila melanogaster) to promote infection of Drosophila cells by a pseudotyped vertebrate retrovirus vector.     

Evolution and phylogeny of old world deer

The phylogenetic pattern and timing of the radiation of Old World deer was determined based on the complete mitochondrial cytochrome b gene from 33 Cervinae taxa. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support was achieved for monophyly of the Old World deer with muntjacs as sister group as well as for the divergence of at least three distinct genera: Rucervus, Dama, and Cervus. The latter clade comprises what have previously been regarded as the genera or subgenera Panolia, Rusa, Cervus, Sika, and probably Przewalskium. Our data also consistently confirmed paraphyly of nominate C. elaphus and did not support the monophyly of Axis. We used these molecular phylogenies to assess the homoplastic evolution of morphological, geographical, ecological, and selected behavioural character state differences within the Cervinae. Reliable fossil calibrations, large molecular data sets, and improved dating methods are shaping a molecular time scale for the evolutionary radiation of Old World deer that occurred at the Miocene/Pliocene transition and is largely compatible with existing palaeontological evidence. Using node ages estimated from sequence data, we estimated an average per-lineage diversification rate of 0.51+/-0.1 species per million years (my) over roughly the last 6 mya.     

Evolution of the Simiiformes and the phylogeny of human chromosomes

Summary This paper is based on the results of Primate chromosome studies obtained using high resolution techniques in our and other laboratories. We discuss the origin and the evolution of the chromosomes in the human karyotype and the time in evolution of the Simiiformes when they acquired their present morphology. Our results indicate that the chromosomes that underwent a higher number of reorganizations during the evolution of the Simiiformes coincide with the chromosomes most often implicated in human chromosome pathology. We describe the main reorganizations that took place during Primate evolution. Centromere activation and inactivation and heterochromatin changes are discussed as mechanisms of chromosome evolution.     

The phylogeny of Goussia and Choleoeimeria (Apicomplexa; Eimeriorina) and the evolution of excystation structures in coccidia

The phylogenetic relationships of Goussia janae and Choleoeimeria sp. were analyzed using the small subunit ribosomal RNA gene (SSU rDNA). This is a first attempt to study the molecular phylogeny of coccidian genera parasitizing strictly poikilotherm hosts. The biliary Eimeria-like coccidia of reptiles classified into the genus Choleoeimeria form a sister clade to the family Eimeriidae, which confirms the separate generic status of the genus Choleoeimeria. The position of Goussia is less robustly resolved, since it forms a trichotomy with the Eimeriidae and Sarcocystidae, or alternatively constitutes the earliest branch of the coccidian lineage. Morphological similarities, namely the extracytoplasmic location of the endogenous stages, and the presence of sutures in the sporocyst wall are discussed in the context of the traditional classification of eimeriids. In contrast to the morphology-based systematics, the monophyly of Goussia and Choleoeimeria is not supported by the SSU rDNA data.     

Evolution of immunoglobulin allotypes and phylogeny of apes

Serum samples from 72 Pan troglodytes, 5 Pan paniscus, 22 Gorilla gorilla, 23 Pongo pygmaeus abelii, 5 Pongo pygmaeus pygmaeus, 2 hybrids P.p. abelii X P.p. pygmaeus and 13 Hylobates lar were tested for Gm(1, 2, 3, 5, 6, 10, 11, 13, 14, 15, 16, 17, 21, 24, 28), Km(1) and Bm(1, 2, 3, 4, 5, 6, 7, 8) immunoglobulin allotypes by the classical hemagglutination inhibition method. The distribution of the various alleles and phenotypes makes it possible to distinguish each species or subspecies. Common chimpanzees have the richest polymorphism. Pygmy chimpanzees share common phenotypes with gorillas. Bornean and Sumatran orangutans have their own patterns of polymorphism, as do gibbons. Our principal component plot and dendrogram are compatible with the traditional classification of Hominoidea [e.g. Simpson, Bull. Am. Mus. nat. Hist. 85: 1-350, 1945] in 3 families: Hominidae, Pongidae and Hylobatidae.     

Evolution of the recA gene and the molecular phylogeny of bacteria

The DNA sequences of the recA gene from 25 strains of bacteria are known. The evolution of these recA gene sequences, and of the derived RecA protein sequences, is examined, with special reference to the effect of variations in genomic G + C content. From the aligned RecA protein sequences, phylogenetic trees have been drawn using both distance matrix and maximum parsimony methods. There is a broad concordance between these trees and those derived from other data (largely 16S ribosomal RNA sequences). There is a fair degree of certainty in the relationships among the Purple or Proteobacteria, but the branching pattern between higher taxa within the eubacteria cannot be reliably resolved with these data. Correspondence to: A.T. Lloyd     

Evolution and phylogeny of gonad morphology in bony fishes

Gonad morphology at the gross anatomical or histological levelshas long been studied by fisheries biologists to identify annualreproductive cycles and length of breeding season, among othergoals. Comparative surveys across vertebrate taxa have not beendetailed enough, however, to describe fully the differencesand similarities among gonads of bony fishes and other vertebrates,and to use gonad morphology in phylogenetic systematic analyses.An emerging constant among vertebrates is the presence of agerminal epithelium composed of somatic and germ cells in bothmales and females. In females, the germinal epithelium linesthe ovarian lamellae. In males, arrangement of the germinalepithelium into compartments varies among osteichthyans: basaltaxa have an anastomosing tubular testis, whereas derived taxahave a lobular testis. The lobular testis is proposed as a synapomorphyof the Neoteleostei. The annual reproductive cycle is hypothesizedto be the source of morphological variation among testis types.Elongation of germinal compartments during early maturationmay result in a transition from anastomosing tubular to lobulartestes. In all male atherinomorphs surveyed, spermatogonia arerestricted to the distal termini of lobules rather than beingdistributed along the lobule; there is an epithelioid arrangementof Sertoli and germ cells rather than a germinal epithelium.Arrest of the maturation-regression phases is hypothesized tolead to formation of the atherinomorph testis. Atherinomorphsalso have a distinctive egg with fluid, rather than granular,yolk. Variation among germinal epithelia is interpreted in adeveloping phylogenetic framework to understand evolution ofgonad morphology and to propose gonad characters for phylogeneticanalyses.     

Evolution and phylogeny of the heterogeneous cytosolic SSU rRNA genes in the genus Plasmodium

Unlike other eukaryotes, malaria parasites in the genus Plasmodium have structurally and functionally different paralogous copies of the cytosolic (cyto-) SSU rRNA (18S rRNA) gene that are expressed at different developmental stages. In P. falciparum, P. vivax, and P. berghei, A-type cyto-SSU rRNA is expressed in asexual stage, while S-type in sporozoite stage. A third type (O-type) has been described in P. vivax. It is expressed only in oocyst stage in the mosquito. Recently, it has been shown that the maintenance of heterogeneous cyto-SSU rRNAs in Plasmodium can be modeled as a birth-and-death process under strong purifying selection [Rooney, A.P., 2004. Mechanisms underlying the evolution and maintenance of functionally heterogeneous 18S rRNA genes in Apicomplexans. Mol. Biol. Evol. 21, 1704-1711]. In this study, we performed detailed phylogenetic analyses of Plasmodium cyto-SSU rRNAs with special emphasis on the evolution of multi-copy genes in simian Plasmodium species. We sequenced paralogous copies of the cyto-SSU rRNA genes from an African simian Plasmodium species, P. gonderi, and Asian simian Plasmodium species, P. fragile, P. coatneyi, P. inui, P. hylobati, P. fieldi, P. simiovale, and P. cynomolgi. Interestingly, all Asian simian Plasmodium species have a single S-type-like gene and several A-type-like genes. Alignment analysis demonstrated for the first time that an approximately 50-residue insertion in the V7 variable region near the stem 43 is shared exclusively by the S-type-like sequences of the Asian simian Plasmodium species and the S- and O-type sequences of P. vivax. We comprehensively analyzed all cyto-SSU rRNA sequences of the genus Plasmodium currently available in the database. Phylogenetic analyses of all publicly available cyto-SSU rRNA sequences for the genus Plasmodium clearly demonstrated that gene duplication events giving rise to A- and S-type-like sequences took place independently at least three times in the Plasmodium evolution, supporting the hypothesis that these genes evolve according to a birth-and-death model.     

Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny

Although the possibility of gene evolution by domain rearrangements has long been appreciated, current methods for reconstructing and systematically analyzing gene family evolution are limited to events such as duplication, loss, and sometimes, horizontal transfer. However, within the Drosophila clade, we find domain rearrangements occur in 35.9% of gene families, and thus, any comprehensive study of gene evolution in these species will need to account for such events. Here, we present a new computational model and algorithm for reconstructing gene evolution at the domain level. We develop a method for detecting homologous domains between genes and present a phylogenetic algorithm for reconstructing maximum parsimony evolutionary histories that include domain generation, duplication, loss, merge (fusion), and split (fission) events. Using this method, we find that genes involved in fusion and fission are enriched in signaling and development, suggesting that domain rearrangements and reuse may be crucial in these processes. We also find that fusion is more abundant than fission, and that fusion and fission events occur predominantly alongside duplication, with 92.5% and 34.3% of fusion and fission events retaining ancestral architectures in the duplicated copies. We provide a catalog of ～9,000 genes that undergo domain rearrangement across nine sequenced species, along with possible mechanisms for their formation. These results dramatically expand on evolution at the subgene level and offer several insights into how new genes and functions arise between species.     

Evolution of the lipocalin family as inferred from a protein sequence phylogeny

The lipocalins constitute a family of proteins that have been found in eubacteria and a variety of eukaryotic cells, where they play diverse physiological roles. It is the primary goal of this review to examine the patterns of change followed by lipocalins through their complex history, in order to stimulate scientists in the field to experimentally contrast our phylogeny-derived hypotheses. We reexamine our previous work on lipocalin phylogeny and update the phylogenetic analysis of the family. Lipocalins separate into 14 monophyletic clades, some of which are grouped in well supported superclades. The lipocalin tree was rooted with the bacterial lipocalin genes under the assumption that they have evolved from a single common ancestor with the metazoan lipocalins, and not by horizontal transfer. The topology of the rooted tree and the species distribution of lipocalins suggest that the newly arising lipocalins show a higher rate of amino acid sequence divergence, a higher rate of gene duplication, and their internal pocket has evolved towards binding smaller hydrophobic ligands with more efficiency.     

Evolution of a centromeric satellite DNA and phylogeny of lacertid lizards.

1. The composition and phyletic distribution of a highly repetitive satellite DNA, isolated from Podarcis sicula, was studied. 2. This DNA was rich in adenine and thymine and displayed frequent adenine stretches. It was always located on the centromeric heterochromatin even in quite taxonomically distant species. 3. Southern blot hybridization of the Taq I satellite on various species of lacertid families showed a close affinity among Podarcis, Algyroides and Lacerta dugesii. 4. All the other taxa investigated did not seem to possess this repeated sequence.     

Evolution of the trypanorhynch tapeworms: Parasite phylogeny supports independent lineages of sharks and rays

Trypanorhynch tapeworms (Platyhelminthes: Cestoda) are among the most diverse and abundant groups of metazoan parasites of elasmobranchs and are a ubiquitous part of the marine food webs that include these apex predators. Here we present a comprehensive analysis of their phylogeny, character evolution and host associations based on 10 years of sampling effort, including representatives of 12 of 15 and 44 of 66 currently recognized trypanorhynch families and genera, respectively. Using a combination of ssrDNA and lsrDNA (Domains 1-3) for 79 and 80 taxa, respectively, we maintain one-to-one correspondence between molecules and morphology by scoring 45 characters from the same specimens used for sequencing, and provide museum vouchers for this material. Host associations are examined through likelihood-based ancestral character state reconstructions (ACSRs) and by estimating dates of divergence using strict and relaxed molecular clock models in a Bayesian context. Maximum parsimony and Bayesian inference analyses of rDNA produced well-resolved and strongly supported trees in which the trypanorhynchs formed two primary lineages and were monophyletic with respect to the diphyllidean outgroup taxa. These lineages showed marked differences in their rates of divergence which in turn resulted in differing support and stability characteristics within the lineages. Mapping of morphological characters onto the tree resulting from combined analysis of rDNA showed most traits to be highly plastic, including some previously considered of key taxonomic importance such as underlying symmetries in tentacular armature. The resulting tree was found to be congruent with the most recent morphologically based superfamily designations in the order, providing support for four proposed superfamilies, but not for the Tentacularioidea and Eutetrarhynchoidea. ACSRs based on the combined analysis of rDNA estimated the original hosts of the two primary parasite lineages to be alternatively rajiform batoids and carcharhiniform sharks. This fundamental split provides independent support for rejecting the notion that rays are derived sharks, and thus supports the most recent molecular phylogenies of the Neoselachii. Beyond the basal split between shark- and ray-inhabiting lineages, no pattern was found to suggest that the trypanorhynchs have closely tracked the evolutionary histories of these host lineages, but instead, it appears that host-switching has been common and that the subsequent evolution of the parasites has been ecologically driven primarily through overlap in the niches of their shark and ray hosts. Using a relaxed molecular clock model calibrated by means of host fossil data, the ray-inhabiting lineage is estimated to have diversified around the Jurassic-Cretaceous boundary, whereas the shark-inhabiting lineage is estimated to have diversified later, in the Middle Cretaceous. Although the large error associated with the estimated divergence dates prevents robust conclusions from being drawn, the dates are nevertheless found to be consistent in a relative sense with the origins of their major hosts groups. The erection and definition of the suborders Trypanobatoida and Trypanoselachoida, for the major clades of trypanorhynchs parasitizing primarily rays and sharks, respectively, is proposed for the two primary lineages recovered here.