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.     

A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species

Evaluating trait correlations across species within a lineage via phylogenetic regression is fundamental to comparative evolutionary biology, but when traits of interest are derived from two sets of lineages that coevolve with one another, methods for evaluating such patterns in a dual‐phylogenetic context remain underdeveloped. Here, we extend multivariate permutation‐based phylogenetic regression to evaluate trait correlations in two sets of interacting species while accounting for their respective phylogenies. This extension is appropriate for both univariate and multivariate response data, and may use one or more independent variables, including environmental covariates. Imperfect correspondence between species in the interacting lineages can also be accommodated, such as when species in one lineage associate with multiple species in the other, or when there are unmatched taxa in one or both lineages. For both univariate and multivariate data, the method displays appropriate type I error, and statistical power increases with the strength of the trait covariation and the number of species in the phylogeny. These properties are retained even when there is not a 1:1 correspondence between lineages. Finally, we demonstrate the approach by evaluating the evolutionary correlation between traits in fig species and traits in their agaonid wasp pollinators. R computer code is provided.     

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.     

Molecular characterization and phylogenetic analysis of Fasciola hepatica from Peru

The causative agent of fasciolosis in South America is thought to be Fasciola hepatica. In this study, Fasciola flukes from Peru were analyzed to investigate their genetic structure and phylogenetic relationships with those from other countries. Fasciola flukes were collected from the three definitive host species: cattle, sheep, and pigs. They were identified as F. hepatica because mature sperms were observed in their seminal vesicles, and also they displayed Fh type, which has an identical fragment pattern to F. hepatica in the nuclear internal transcribed spacer 1. Eight haplotypes were obtained from the mitochondrial NADH dehydrogenase subunit 1 (nad1) sequences of Peruvian F. hepatica; however, no special difference in genetic structure was observed between the three host species. Its extremely low genetic diversity suggests that the Peruvian population was introduced from other regions. Nad1 haplotypes identical to those of Peruvian F. hepatica were detected in China, Uruguay, Italy, Iran, and Australia. Our results indicate that F. hepatica rapidly expanded its range due to human migration. Future studies are required to elucidate dispersal route of F. hepatica from Europe, its probable origin, to other areas, including Peru.     

寄生虫及其宿主协同进化的研究进展

本文对寄生虫及其宿主协同进化的研究进行了回顾,将其发展分为三个阶段：1．寄生虫-宿主协同进化的初步认识;2．协同进化模式及其内在机制的探索;3．协同进化机制研究方法的发展。目前的研究主要集中于协同进化生物学意义的进一步深入探讨。同时,对协同进化的有关概念、方法和本学科的发展进行了简单阐述和讨论。     

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.     

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.     

Molecular markers for phylogenetic applications derived from comparative plastome analysis of Prunus species

Interspecific and intergeneric relationships of Prunus s.l. are still unclear due to low levels of genetic variation among species, and resulting partially unresolved phylogenetic inferences. Here we sequenced and compared six complete plastomes from two subgenera of Prunus in order to choose molecular markers to increase the amount of genetic variation suitable for inference of Prunus phylogeny. The plastomes range between 157 817 and 158 995 bp in length, and we found different levels of inverted repeat (IR) contraction among the three sampled subgenera of Prunus s.l. Most regions in Prunus plastomes considered individually provide low phylogenetic resolution at the subgenus or species level compared to a tree constructed using all 78 coding regions combined. We compared levels of variation among 206 coding regions and noncoding (intergenic and intron) plastid regions and inferred phylogenies from each region considered individually. We then chose using two regions together for future studies of relationships in Prunus, ycf1 and trnT-L, that display high to moderate levels of variation among coding and intergenic regions, respectively, and that individually permit inference of resolved species-level trees in Prunus with moderate to strong branch support. Considered together, these two regions allow inference of the same topology of Prunus inferred using all coding plastid regions combined, with comparable levels of tree support to the full plastome set. These two loci should therefore be useful as a plastid phylogenetic marker set for further inference of relationships within Prunus s.l.     

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.     

Escaping the matrix: a new algorithm for phylogenetic comparative studies of co-evolution

An algorithm for generating host cladograms from parasite‐host cladograms derived from parasite phylogenies, Phylogenetic Analysis for Comparing Trees (PACT), is described. PACT satisfies Assumption 0, that all the information in each parasite‐host cladogram must be used in a co‐evolutionary analysis, and that the host relationships depicted in the final host cladogram must be logically consistent with the phylogenetic relationships depicted in every part of every parasite‐host cladogram used to construct the host cladogram. It accounts for cases of speciation by host switching and expansion of host range, and reticulated host relationships, in addition to co‐speciation, sympatric speciation, and extinction in all input parasite‐host cladograms, and does so without a priori weighting schemes and without a posteriori manipulation of the data.     

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.     

Begging call matching between a specialist brood parasite and its host: a comparative approach to detect coevolution

Studies of avian brood parasite systems have typically investigated the mimicry of host eggs by specialist parasites. Yet, several examples of similarity between host and parasite chick appearance or begging calls suggest that the escalation of host–parasite arms races may also lead to visual or vocal mimicry at the nestling stage. Despite this, there have been no large-scale comparative studies of begging calls to test whether the similarity of host and parasite is greater than predicted by chance or phylogenetic distance within a geographically distinct species assemblage. Using a survey of the begging calls of all native forest passerines in New Zealand, we show that the begging call of the host-specialist shining cuckoo ( Chrysococcyx lucidus ) is most similar to that of its grey warbler ( Gerygone igata ) host compared to any of the other species, and that this is unlikely to have occurred by chance. Randomization tests revealed that the incorporation of the shining cuckoo's begging calls into our species-set consistently reduced the phylogenetic signal within cluster trees based on begging call similarity. By contrast, the removal of the grey warbler calls did not reduce the phylogenetic signal in the begging call similarity trees. These two results support a scenario in which coevolution of begging calls has not taken place: the begging call of the host retains its phylogenetic signal, whereas that of the parasite has changed to match that of its host.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 208–216.     

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.     

Extending phylogenetic studies of coevolution: secondary Brooks parsimony analysis, parasites, and the Great Apes

Dowling recently compared the empirical properties of Brooks parsimony analysis (BPA) and the leading method for studying phylogenetic aspects of coevolution, reconciled tree analysis (using the computer program TreeMap), based on a series of simulations. Like the majority of authors who have compared BPA with other methods, however, Dowling considered only the form of BPA proposed in 1981 and did not take into account various modifications of the method proposed from 1986 to 2002. This leaves some doubt as to the robustness of his assessments of both the superiority of BPA and its shortcomings. We provide a précis of the principles of contemporary BPA, including ways to implement it algorithmically, using either Wagner algorithm‐based or Hennigian argumentation‐based approaches, followed by an empirical example. Our study supports Dowling's fundamental conclusions about the superiority of primary BPA relative to TreeMap. However, his conclusions about the shortcomings of BPA due to inclusive ORing (i.e., the production of ghost taxa) are incorrect, as secondary BPA eliminates inclusive ORing from the method. Secondary BPA provides a more complete account of the evolutionary associations between the parasite groups and their hosts than does primary BPA, without sacrificing any indirectly generated information about host phylogeny. Secondary BPA of two groups of nematodes inhabiting Great Apes shows that TreeMap analysis underestimated the amount of cospeciation in the evolution of the nematode genus Enterobius.     

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.     

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.