Brain structure evolution in a basal vertebrate clade: evidence from phylogenetic comparative analysis of cichlid fishes

Background  

The vertebrate brain is composed of several interconnected, functionally distinct structures and much debate has surrounded the basic question of how these structures evolve. On the one hand, according to the 'mosaic evolution hypothesis', because of the elevated metabolic cost of brain tissue, selection is expected to target specific structures mediating the cognitive abilities which are being favored. On the other hand, the 'concerted evolution hypothesis' argues that developmental constraints limit such mosaic evolution and instead the size of the entire brain varies in response to selection on any of its constituent parts. To date, analyses of these hypotheses of brain evolution have been limited to mammals and birds; excluding Actinopterygii, the basal and most diverse class of vertebrates. Using a combination of recently developed phylogenetic multivariate allometry analyses and comparative methods that can identify distinct rates of evolution, even in highly correlated traits, we studied brain structure evolution in a highly variable clade of ray-finned fishes; the Tanganyikan cichlids.     

Host-parasite coevolution: comparative evidence for covariation of life history traits in primates and oxyurid parasites.

The environmental factors that drive the evolution of parasite life histories are mostly unknown. Given that hosts provide the principal environmental features parasites have to deal with, and given that these features (such as resource availability and immune responses) are well characterized by the life history of the host, we may expect natural selection to result in covariation between parasite and host life histories. Moreover, some parasites show a high degree of host specificity, and cladistic analyses have shown that host and parasite phylogenies can be highly congruent. These considerations suggest that parasite and host life histories may covary. The central argument in the theory of life history evolution concerns the existence of trade-offs between traits. For parasitic nematodes it has been shown that larger body sizes induce higher fecundity, but this is achieved at the expense of delayed maturity. As high adult mortality would select for reduced age at maturity, the selective benefit of increased fecundity is expressed only if adult mortality is low. Parasite adult mortality may depend on a number of factors, including host longevity. Here we tested the hypothesis concerning the positive covariation between parasite body size (which reflects parasite longevity) and host longevity. To achieve this goal, we used the association between the pinworms (Oxyuridae, Nematoda) and their primate hosts. Oxyurids are highly host specific and are supposed to be involved in a coevolutionary process with their hosts. We found that female parasite body length was positively correlated with host longevity after correcting for phylogeny and host body mass. Conversely, male parasite body length and host longevity were not correlated. These results confirm that host longevity may represent a constraint on the evolution of body size in oxyurids, at least in females. The discrepancy between female and male oxyurids is likely to depend on the particular mode of reproduction of this taxon (haplodiploidy), which should result in weak (or even null) selection pressures to an increase of body size in males.     

A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide

Cladistic parsimony analyses of rbcL nucleotide sequence data from 171 taxa representing nearly all tribes and subtribes of Orchidaceae are presented here. These analyses divide the family into five primary monophyletic clades: apostasioid, cypripedioid, vanilloid, orchidoid, and epidendroid orchids, arranged in that order. These clades, with the exception of the vanilloids, essentially correspond to currently recognized subfamilies. A distinct subfamily, based upon tribe Vanilleae, is supported for Vanilla and its allies. The general tree topology is, for the most part, congruent with previously published hypotheses of intrafamilial relationships; however, there is no evidence supporting the previously recognized subfamilies Spiranthoideae, Neottioideae, or Vandoideae. Subfamily Spiranthoideae is embedded within a single clade containing members of Orchidoideae and sister to tribe Diurideae. Genera representing tribe Tropideae are placed within the epidendroid clade. Most traditional subtribal units are supported within each clade, but few tribes, as currently circumscribed, are monophyletic. Although powerful in assessing monophyly of clades within the family, in this case rbcL fails to provide strong support for the interrelationships of the subfamilies (i.e., along the spine of the tree). The cladograms presented here should serve as a standard to which future morphological and molecular studies can be compared.     

Vitamin E biosynthesis genes in rice: Molecular characterization, expression profiling and comparative phylogenetic analysis

Vitamin E comprises four tocopherols and four tocotrienols, collectively termed tocochromanols that play an essential role as antioxidants in humans, animals and photosynthetic organisms and are also believed to play a role in modulation of signal transduction and gene expression pathways. In rice and Populus genome, we have identified 7 and 11 tocochromanol biosynthesis genes, respectively. A detailed study of domain organization and phylogenetic analysis of these genes in rice, Arabidopsis and other plants has revealed the presence of homologous genes. Expression profiling of rice and Populus genes has been done by full-length cDNA and EST-based analysis. In rice, real-time PCR analysis was done to reveal the light-regulated expression pattern. Microarray-based expression analysis in different rice tissues and developmental stages revealed expression of these genes in almost all plant tissues/organs. Under abiotic stress conditions, expression of gene coding for HPPD enzyme, that regulates pathway flux, was also found to be increased. This information is expected to be helpful for further functional characterization of tocochromanol biosynthesis genes in different plant tissues under diverse growth conditions.     

The phylogenetic placement of Chondrichthyes: inferences from analysis of multiple genes and implications for comparative studies

Elasmobranch fishes (sharks and rays) have proven valuable for inferring general and specific properties of molecular evolution through comparative studies with crown group vertebrates because they are the most ancient group of gnathostomes. Recent studies have questioned the conventional phylogenetic placement of sharks in the vertebrate tree, however. In this paper I review the importance of the basal position of Chondrichthyes for comparative biology and compile evidence from multiple, independent genes to evaluate the phylogenetic placement of sharks. The results suggests that alternative phylogenetic hypotheses of the relationships among the Chondrichthyes, Actinopterygii and Sarcopterygii can not be refuted with available data, implying that the assumption of the basal placement of sharks in the vertebrate tree is suspect. Resolving the phylogeny of basal vertebrates is important for testing hypotheses about the evolution of vertebrates, and the current lack of a robust phylogeny limits evolutionary inferences that can be gained from comparative studies that include sharks and rays.     

Dispersal process driving subtropical forest reassembly: evidence from functional and phylogenetic analysis

Understanding the mechanisms of secondary succession related to forest management practices is receiving increasing attention in community ecology and biodiversity conservation. Abiotic and biotic filtering are deterministic processes driving community reassembly. A functional trait or phylogeny-based approach predicts that environmental filtering induced by clearcut-logging results in functional/phylogenetic clustering in younger forests, while biotic filtering (competitive exclusion) promotes functional/phylogenetic overdispersion in old-growth forests. From this perspective, we examined the patterns of functional/phylogenetic structures using tree community data (147 species × 170 plots). These data were chronosequenced from clearcut secondary forests to old-growth subtropical forests in the Ryukyu Archipelago, with species’ trait data (leaf and stem) and species level phylogeny. To detect clustering or overdispersion in the functional and phylogenetic structures, we calculated the standardized effect size of mean nearest trait distance and mean nearest phylogenetic distance within the plots. Functional or phylogenetic clustering was relatively weak in secondary forests, and their directional change with increasing forest age was not generally detected. Mean nearest trait/phylogenetic distance for most plots fell within the range of random expectation. The results suggest that abiotic/biotic filtering related to functional traits or phylogenetic relatedness plays a diminished role in shaping species assembly during secondary succession in the subtropical forest. Our findings of functional and phylogenetic properties might shed light on the importance of dispersal (stochastic) processes in the regional species pool during community reassembly after anthropogenic disturbance. It will also contribute to the development of coordinated schemes that maintain potential species assembly processes in the subtropical forest.     

On the coevolution of pathogen and host: I. General theory of discrete time coevolution

The theory of discrete time models of genetically conditioned coevolution is considered as an extension of classical population genetics theory. Strengths and weaknesses of the underlying assumptions are critically discussed in the context of host-pathogen interactions. Convenient formulae are provided to analyze the stability of equilibria. Some conclusions are drawn, which depend only on fairly general assumptions about the nature of host-pathogen coevolution.     

Congruent evidence from alpha-tubulin and beta-tubulin gene phylogenies for a zygomycete origin of microsporidia

The origin of microsporidia and the evolutionary relationships among the major lineages of fungi have been examined by molecular phylogeny using alpha-tubulin and beta-tubulin. Chytrids, basidiomycetes, ascomycetes, and microsporidia were all recovered with high support, and the zygomycetes were consistently paraphyletic. The microsporidia were found to branch within zygomycetes, and showed relationships with members of the Entomophthorales and Zoopagales. This provides support for the microsporidia having evolved from within the fungi, however, the tubulin genes are difficult to interpret unambiguously since fungal and microsporidian tubulins are very divergent. Rapid evolutionary rates a characteristic of practically all microsporidian genes studied, so determining their evolutionary history will never be completely free of such difficulties. While the tubulin phylogenies do not provide a decisive conclusion, they do further narrow the probable origin of microsporidia to a zygomycete-like ancestor.     

Six new species of microsporidia of the genus Amblyospora (Microspora: Amblyosporidae) from blood sucking mosquitoes (Diptera: Culicidae) from the west Siberia

Microsporidia of the genus Amblyospora parasiting the adipose body of mosquito larvae of the genus Aedes and Culex has been studied with both light and electron microscopy. Six new species of microsporidia are described based on ultrastructural characteristics of spores and sporogony stages. Amblyospora flavescens sp. n. Mature spores are egg-shaped. The spore wall with three layers, about 165 nm. Exospore is two-membranous. Subexospore is absent. Endospore is electron-translucent. Polaroplast consists of three parts: lamellar, large vesicular, lamellar. The anisofilar polar filament with 10--11 coils (3 1/2 + 2 1/2 + 4-5). Fixed spores are 6.3 +/- 0.1 x 4.24 +/- 0.1 microm. Amblyospora kolarovi sp. n. Mature spores are egg-shaped. The spore wall with three layers, about 265-315 nm. Exospore shapes tucks on the surface of spore. It is two-membranous. Subexospore is quagge, structural. Endospore is electron-translucent. Polaroplast consists of two parts: lamellar and large vesicular. The anisofilar polar filament with 11-13 coils (3 + 8-10). Fixed spores are 5.4-5.6 x 3.5-4.2 microm. Amblyospora orbiculata sp. n. Mature spores are widely egg-shaped. On a back pole there is a small concavity. The spore wall with three layers, about 155 nm. Exospore is shapes tucks on a surface of spore. It is two-membranous. Subexospore is absent. Endospore is electron-translucent. Polaroplast consists of three parts: lamellar, vesicular, lamellar. Polar filament is anisofilar, with 11 1/2 coils (4 1/2 + 1 + 6). Fixed spores are 6.3 +/- 0.1 x x 4.0 +/- 0.1 microm. Amblyospora rugosa sp. n. Mature spores are egg-shaped. On a back pole there is a small concavity. The spore wall with three layers, about 225 nm. Exospore is shapes tucks on a surface of spore. It is two-membranous. Subexospore is quaggy, structural. Endospore is electron-translucent. Polaroplast lamellate. Polar filament is anisofilar, with 17 1/2 coils (3 1/2 + 1 + 13). Fixed spores are 5.3 +/- 0.1 x 3.7 +/- 0.1 microm. Amblyospora undata sp. n. Mature spores are egg-shaped. The spore wall is three-layered, about 220 nm. Exospore is shapes tucks on a surface of spore. It is two-membranous. Subexospore is quaggy, structural. Endospore is electron-translucent. Polaroplast lamellate. The anisofilar polar filament with 8 coils (3 + 5). Fixed spores are 5.0 +/- 0.1 x 3.0 +/- 0.1 microm. Amblyospora urski sp. n. Mature spores have widely oval form. The back pole is concave. The spore wall with three layers, about 280 nm. Exospore is shapes tucks on a surface of spore. It is two-membranous. Subexospore is quaggy, structural. Endospore is electron-translucent. Polaroplast lamellate. Polar filament is anisofilar, with 6 coils (2 + 4). Fixed spores are 4.4 +/- 0.1 x 2.9 +/- 0.1 microm.     

Dissecting the fungal biology of Bipolaris papendorfii: from phylogenetic to comparative genomic analysis

Bipolaris papendorfii has been reported as a fungal plant pathogen that rarely causes opportunistic infection in humans. Secondary metabolites isolated from this fungus possess medicinal and anticancer properties. However, its genetic fundamental and basic biology are largely unknown. In this study, we report the first draft genome sequence of B. papendorfii UM 226 isolated from the skin scraping of a patient. The assembled 33.4 Mb genome encodes 11,015 putative coding DNA sequences, of which, 2.49% are predicted transposable elements. Multilocus phylogenetic and phylogenomic analyses showed B. papendorfii UM 226 clustering with Curvularia species, apart from other plant pathogenic Bipolaris species. Its genomic features suggest that it is a heterothallic fungus with a putative unique gene encoding the LysM-containing protein which might be involved in fungal virulence on host plants, as well as a wide array of enzymes involved in carbohydrate metabolism, degradation of polysaccharides and lignin in the plant cell wall, secondary metabolite biosynthesis (including dimethylallyl tryptophan synthase, non-ribosomal peptide synthetase, polyketide synthase), the terpenoid pathway and the caffeine metabolism. This first genomic characterization of B. papendorfii provides the basis for further studies on its biology, pathogenicity and medicinal potential.     

A new Y-tube olfactometer for mosquitoes to measure the attractiveness of host odours

The behavioural responses of flying western flower thrips (Frankliniella occidentalis Pergande) (Thysanoptera: Thripidae) to the colour yellow and the odour anisaldehyde were examined. In a wind tunnel, upwind flight by female thrips was common in an airflow of 0.11 m s^–1 but was impeded at 0.22 m s^–1. In the absence of anisaldehyde, flying female thrips exhibited an oriented response towards a yellow cue in the wind tunnel at a wind speed of 0.11 m s^–1. The main response of females to anisaldehyde in the wind tunnel was flight inhibition. There was no evidence of an odour-induced visual response, an odour-induced anemotactic response or chemotaxis by female thrips to anisaldehyde in wind tunnel bioassays, but chemokinesis was implicated. With a matrix of yellow or black water traps with and without anisaldehyde in a greenhouse sweet pepper crop, yellow traps with anisaldehyde caught more thrips adults than yellow traps without anisaldehyde, black traps with anisaldehyde and black traps without anisaldehyde (1.3, 28 and 721 times for males respectively and 2.4, 9 and 117 times for females, respectively). Differences between respective traps were statistically significant in almost all cases. Trapping experiments using a centre-baited trap design to reduce the interaction of anisaldehyde between baited and unbaited traps were undertaken in tomato and sweet pepper greenhouse crops. When the spatial distribution of the thrips adult population within the greenhouse was taken into account, yellow water traps with anisaldehyde caught between 11 and 15 times more female and 3 and 20 times more male F. occidentalis adults than yellow traps without anisaldehyde.     

Networks in phylogenetic analysis: new tools for population biology

Phylogenetic analysis has changed greatly in the past decade, including the more widespread appreciation of the idea that evolutionary histories are not always tree-like, and may, thus, be best represented as reticulated networks rather than as strictly dichotomous trees. Reconstructing such histories in the absence of a bifurcating speciation process is even more difficult than the usual procedure, and a range of alternative strategies have been developed. There seem to be two basic uses for a network model of evolution: the display of real but unobservable evolutionary events (i.e. a hypothesis of the true phylogenetic history), and the display of character conflict within the data itself (i.e. a summary of the data). These two general approaches are briefly reviewed here, and the strengths and weaknesses of the different implementations are compared and contrasted. Each network methodology seems to have limitations in terms of how it responds to increasing complexity (e.g. conflict) in the data, and therefore each is likely to be more appropriate for one of the two uses than for the other. Several examples using parasitological data sets illustrate the uses of networks within the context of population biology.     

PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families

Summary: Malaria, one of the world's most common diseases, iscaused by the intracellular protozoan parasite known as Plasmodium.Recently, with the arrival of several malaria parasite genomes,we established an integrated system named PlasmoGF for comparativegenomics and phylogenetic analysis of Plasmodium gene families.Gene families were clustered using the Markov Cluster algorithmimplemented in TribeMCL program and could be searched usingkeywords, gene-family information, domain composition, GeneOntology and BLAST. Moreover, a number of useful bioinformaticstools were implemented to facilitate the analysis of these putativePlasmodium gene families, including gene retrieval, annotation,sequence alignment, phylogeny construction and visualization.In the current version, PlasmoGF contained 8980 sets of genefamilies derived from six malaria parasite genomes: Plasmodium.falciparum, P. berghei, P. knowlesi, P. chabaudi, P. vivax andP. yoelii. The availability of such a highly integrated systemwould be of great interest for the community of researchersworking on malaria parasite phylogenomics. Availability: PlasmoGF is freely available at http://bioinformatics.zj.cn/pgf/ Contact: xiaokunli{at}163.net; baoqy{at}genomics.org.cn; fuz3{at}psu.edu Associate Editor: Jonathan Wren The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors.     

Fels-Rand: an Xlisp-Stat program for the comparative analysis of data under phylogenetic uncertainty

MOTIVATION: Currently available programs for the comparative analysis of phylogenetic data do not perform optimally when the phylogeny is not completely specified (i.e. the phylogeny contains polytomies). Recent literature suggests that a better way to analyse the data would be to create random trees from the known phylogeny that are fully-resolved but consistent with the known tree. A computer program is presented, Fels-Rand, that performs such analyses. A randomisation procedure is used to generate trees that are fully resolved but whose structure is consistent with the original tree. Statistics are then calculated on a large number of these randomly-generated trees. Fels-Rand uses the object-oriented features of Xlisp-Stat to manipulate internal tree representations. Xlisp-Stat's dynamic graphing features are used to provide heuristic tools to aid in analysis, particularly outlier analysis. The usefulness of Xlisp-Stat as a system for phylogenetic computation is discussed. AVAILABILITY: Available from the author or at http://www.uq.edu.au/~ansblomb/Fels-Rand.sit.hqx. Xlisp-Stat is available from http://stat.umn.edu/~luke/xls/xlsinfo/xlsinfo.html. CONTACT: s.blomberg@abdn.ac.uk     

The evolution of a female genital trait widely distributed in the Lepidoptera: comparative evidence for an effect of sexual coevolution

Background

Sexual coevolution is considered responsible for the evolution of many male genital traits, but its effect on female genital morphology is poorly understood. In many lepidopterans, females become temporarily unreceptive after mating and the length of this refractory period is inversely related to the amount of spermatophore remaining in their genital tracts. Sperm competition can select for males that delay female remating by transferring spermatophores with thick spermatophore envelopes that take more time to be broken. These envelopes could select for signa, sclerotized sharp structures located within the female genital tract, that are used for breaking spermatophores. Thus, this hypothesis predicts that thick spermatophore envelopes and signa evolve in polyandrous species, and that these adaptations are lost when monandry evolves subsequently. Here we test the expected associations between female mating pattern and presence/absence of signa, and review the scant information available on the thickness of spermatophore envelopes.

Methodology/Principal Findings

We made a literature review and found information on female mating pattern (monandry/polyandry), presence/absence of signa and phylogenetic position for 37 taxa. We built a phylogenetic supertree for these taxa, mapped both traits on it, and tested for the predicted association by using Pagel''s test for correlated evolution. We found that, as predicted by our hypothesis, monandry evolved eight times and in five of them signa were lost; preliminary evidence suggests that at least in two of the three exceptions males imposed monandry on females by means of specially thick spermatophore envelopes. Previously published data on six genera of Papilionidae is in agreement with the predicted associations between mating pattern and the characteristics of spermatophore envelopes and signa.

Conclusions/Significance

Our results support the hypothesis that signa are a product of sexually antagonistic coevolution with spermatophore envelopes.     

Molecular evolution of imprinted genes: no evidence for antagonistic coevolution.

Genomically imprinted genes are those for which expression is dependent on the sex of the parent from which they are derived. Numerous theories have been proposed for the evolution of genomic imprinting: one theory is that it is an intra-individual manifestation of classical parent -offspring conflict. This theory is unique in predicting that an arms race may develop between maternally and paternally derived genes for the control of foetal growth demands. Such antagonistic coevolution may be mediated through changes in the structure of the proteins concerned. Comparable coevolution is the most likely explanation for the rapid changes seen in antigenic components of parasites and antigen recognition components of immune systems. We have examined the evolution of insulin-like growth factor Igf2, and its antagonistic receptor Igf2r) and find that in contrast to immune genes, at the sites of mutual binding they are highly conserved. In addition, we have analysed the rate of molecular evolution of seven imprinted genes including Igf2 and Igf2r), sequenced in both mouse and rat, and had that this is the same as that of nonimprinted receptors and significantly lower than that of immune genes controlling for differences in mutation rates. Contrary to the expectations of the conflict hypothesis, we hence find no evidence for antagonistic coevolution of imprinted genes mediated by changes in sequence.     

Molecular characterization and phylogenetic analysis of Eimeria from turkeys and gamebirds: implications for evolutionary relationships in Galliform birds

In order to determine the evolutionary relationships among Eimeria species that parasitize birds of the Galliformes, the 18s rDNA gene and a portion of the cytochrome oxidase subunit 1 (cox-1) were amplified from Eimeria species isolated from turkeys, chukars, and pheasants. The phylogenetic analysis of these sequences suggests that species infecting chickens are polyphyletic and, therefore, do not all share a direct common ancestor. Both the 18s rDNA and the cox-1 sequences indicate that Eimeria tenella and Eimeria necatrix are more closely related to Eimeria of turkeys and pheasants than to other species that infect the chicken. It is, therefore, likely that the chicken Eimeria spp. represent 2 separate ancestral colonizations of the gut, one of which comprises E. tenella and E. necatrix that infect the ceca, while the other includes Eimeria acervulina, Eimeria brunetti, Eimeria maxima, and Eimeria mitis, which infect the upper regions of the intestine.     

SHORT COMMUNICATION: Little evidence for Cope’s rule from Bayesian phylogenetic analysis of extant mammals

According to Cope’s rule, lineages tend to evolve towards larger body size, possibly because of selective advantages of being large. The status of Cope’s ‘rule’ remains controversial as it is supported in some but not all large‐scale fossil studies. Here, we test for Cope’s rule by Bayesian analyses of average body masses of 3253 extant mammal species on a dated phylogenetic tree. The data favour a model that does not assume Cope’s rule. When Cope’s rule is assumed, the best estimate of its strength is an average ancestor‐descendant increase in body size of only 0.4%, which sharply contrasts with the 9% bias estimated from fossil mammals. Thus, we find no evidence for Cope’s rule from extant mammals, in agreement with earlier analyses of existing species, which also did not find support for Cope’s rule.     

A comparative and phylogenetic analysis of the alpha-actinin rod domain

Alpha-actinin is a ubiquitous actin-binding protein, composed of 3 domains; an actin-binding domain and a calcium-binding domain at the termini, connected by a rod domain composed by 1, 2, or 4 spectrin repeats (SRs). To understand how the rod domain has evolved during evolution, we have analyzed and compared the amino acid residue heterogeneity and phylogeny of the SRs of alpha-actinins of vertebrates, invertebrates, fungi, and several protozoa. The repeats of vertebrate alpha-actinins show a high degree of similarity, whereas repeats of invertebrates, fungi, and, in particular, of protozoa are more divergent. In the phylogeny, SR1 of all species were clustered together, independent of the number of repeats in the protein. It was also obvious that the second and last repeat in fungi (SR2) grouped with the fourth and last repeat of vertebrates and invertebrates (SR4). Therefore, the phylogeny implied that the rod domain of the cenancestral alpha-actinin only contained one SR. It was also obvious that SR2 of fungi are related to SR4 of vertebrates and invertebrates, implying that in the second intragenic duplication 2 repeats (i.e., what become SR2 and SR3) were inserted between the initial 2 repeats that become SR1 and SR4.