Composition and phylogenetic affinities of vangas (Vangidae, Oscines, Passeriformes) based on morphological characters

The first cladistic analysis of the relationship of Malagasy vangas (Vangidae) based on morphological characters is presented here. The comparative morphological analysis provides new arguments for the exclusion of several taxa traditionally or recently assigned to Vangidae such as Tylas 'Vanga' ( Tylas eduardi ), Crossley's Babbler ( Mystacornis crossleyi ) and newtonias ( Newtonia spp.), but also for the exclusion of the Red-tailed 'Vanga' ( Calicalicus madagascariensis ) from the Vangidae. It leads also to the hypothesis that vangas sensu stricto , the Australasian woodswallows (Artamidae) and the Australo-Papuan butcherbirds (Cracticidae) form a monophyletic group, with the New Guinean peltops ( Peltops spp.) as its probable sister taxon. Such a relationship implies that the last common ancestor of vangas reached Madagascar from the east by means of a dispersal event across the Indian Ocean. This hypothesis is partly in accordance with that of William Pycraft (1907) published a century ago, but in conflict with contemporary hypotheses based on DNA sequence analysis which favour helmet-shrikes, bush shrikes and relatives as the closest relatives of vangas and therefore an African origin of this group.     

The intron of tRNA-TrpCCA is dispensable for growth and translation of Saccharomyces cerevisiae

A part of eukaryotic tRNA genes harbor an intron at one nucleotide 3' to the anticodon, so that removal of the intron is an essential processing step for tRNA maturation. While some tRNA introns have important roles in modification of certain nucleotides, essentiality of the tRNA intron in eukaryotes has not been tested extensively. This is partly because most of the eukaryotic genomes have multiple genes encoding an isoacceptor tRNA. Here, we examined whether the intron of tRNA-Trp(CCA) genes, six copies of which are scattered on the genome of yeast, Saccharomyces cerevisiae, is essential for growth or translation of the yeast in vivo. We devised a procedure to remove all of the tRNA introns from the yeast genome iteratively with marker cassettes containing both positive and negative markers. Using this procedure, we removed all the introns from the six tRNA-Trp(CCA) genes, and found that the intronless strain grew normally and expressed tRNA-Trp(CCA) in an amount similar to that of the wild-type genes. Neither incorporation of (35)S-labeled amino acids into a TCA-insoluble fraction nor the major protein pattern on SDS-PAGE/2D gel were affected by complete removal of the intron, while expression levels of some proteins were marginally affected. Therefore, the tRNA-Trp(CCA) intron is dispensable for growth and bulk translation of the yeast. This raises the possibility that some mechanism other than selective pressure from translational efficiency maintains the tRNA intron on the yeast genome.     

Pattern and timing of diversification in Yucca (Agavaceae): specialized pollination does not escalate rates of diversification

The yucca-yucca moth interaction is one of the most well-known and remarkable obligate pollination mutualisms, and is an important study system for understanding coevolution. Previous research suggests that specialist pollinators can promote rapid diversification in plants, and theoretical work has predicted that obligate pollination mutualism promotes cospeciation between plants and their pollinators, resulting in contemporaneous, parallel diversification. However, a lack of information about the age of Yucca has impeded efforts to test these hypotheses. We used analyses of 4322 AFLP markers and cpDNA sequence data representing six non-protein-coding regions (trnT-trnL, trnL, trnL intron, trnL-trnF, rps16 and clpP intron 2) from all 34 species to recover a consensus organismal phylogeny, and used penalized likelihood to estimate divergence times and speciation rates in Yucca. The results indicate that the pollination mutualism did not accelerate diversification, as Yucca diversity (34 species) is not significantly greater than that of its non-moth-pollinated sister group, Agave sensu latissimus (240 species). The new phylogenetic estimates also corroborate the suggestion that the plant-moth pollination mutualism has at least two origins within the Agavaceae. Finally, age estimates show significant discord between the age of Yucca (ca 6-10Myr) and the current best estimates for the age of their pollinators (32-40Myr).     

An endemic radiation of Malagasy songbirds is revealed by mitochondrial DNA sequence data

The bird fauna of Madagascar includes a high proportion of endemic species, particularly among passerine birds (Aves: Passeriformes). The endemic genera of Malagasy songbirds are not allied obviously with any African or Asiatic taxa, and their affinities have been debated since the birds first were described. We used mitochondrial sequence data to estimate the relationships of 13 species of endemic Malagasy songbirds, 17 additional songbird species, and one species of suboscine passerine. In our optimal trees, nine of the 13 Malagasy species form a clade. although these birds currently are classified in three different families. In all optimal trees, the sister to this endemic clade is a group of Old World warblers including both African and Malagasy birds. The endemic Malagasy songbird clade rivals other island radiations, including the vangas of Madagascar and the finches of the Galapagos, in ecological diversity.     

Costly reproductive competition between females in a monogamous cooperatively breeding bird

In many cooperatively breeding societies, only a few socially dominant individuals in a group breed, reproductive skew is high, and reproductive conflict is common. Surprisingly, the effects of this conflict on dominant reproductive success in vertebrate societies have rarely been investigated, especially in high-skew societies. We examine how subordinate female competition for breeding opportunities affects the reproductive success of dominant females in a monogamous cooperatively breeding bird, the Southern pied babbler (Turdoides bicolor). In this species, successful subordinate reproduction is very rare, despite the fact that groups commonly contain sexually mature female subordinates that could mate with unrelated group males. However, we show that subordinate females compete with dominant females to breed, and do so far more often than expected, based on the infrequency of their success. Attempts by subordinates to obtain a share of breeding impose significant costs on dominant females: chicks fledge from fewer nests, more nests are abandoned before incubation begins, and more eggs are lost. Dominant females appear to attempt to reduce these costs by aggressively suppressing potentially competitive subordinate females. This empirical evidence provides rare insight into the nature of the conflicts between females and the resultant costs to reproductive success in cooperatively breeding societies.     

The use of mitochondrial and nuclear sequence data in assessing the taxonomic status of the endangered Uluguru Bush Shrike Malaconotus alius

The endangered Uluguru Bush Shrike Malaconotus alius is a large, black-headed bush shrike, strictly endemic to the Uluguru Mountains in Tanzania. It has recently been suggested that this species has been misplaced within the genus Malaconotus and might instead be related to Malagasy Vangidae. To assess its systematic affinities, we analysed 1518 bp of sequence data obtained from a nuclear intron (myoglobin intron-2) and a mitochondrial protein-coding gene (ND2) using parsimony, maximum likelihood and Bayesian inference. Both genes strongly support the traditional placement within the genus Malaconotus , suggesting that similarities between the Uluguru Bush Shrike and the Vangidae are due to convergence. These results caution that taxonomic changes should not be made without a proper character analysis (i.e. assignment of character homology).     

Four New Species of the Feather Mite Genus Vanginyssus Mironov, 2001 (Astigmata: Pteronyssidae) from the Vangas (Passeriformes: Vangidae) in Madagascar

Four new feather mite species of Vanginyssus Mironov, 2001 are described from vangas (Passeriformes: Vangidae), an endemic passerine family from Madagascar: Vanginyssus euryceros n. sp. from the helmet vanga Euryceros prevostii Lesson, V. madagascarinus n. sp. from the blue vanga Cyanolanius madagascarinus (Linnaeus), V. mystacornis n. sp. from the Crossley’s babbler Mystacornis crossleyi (Grandidier) and V.␣orioliae n. sp. from the Bernier’s vanga Oriolia bernieri Geoffroy Saint-Hilaire. A key to the five known species of Vanginyssus is provided.     

High-throughput sequencing reveals dietary segregation in Malaysian babblers

The coexistence of numerous species within a community results from how those species use available resources. Babblers are one of the major groups of Malaysian insectivorous birds, which frequently forage in dense vegetation cover and have a high level of sympatry. Therefore, examining the diet, prey selection, and niche segregation of babblers can be challenging. In this study, we used high-throughput sequencing to investigate potential dietary overlap or segregation among 10 babbler species of the 4 genera of the family Pellorneidae and Timaliidae: Pellorneum, Malacopteron, Stachyris, and Cyanoderma in central peninsular Malaysia. We tested the hypothesis that trophically similar species may differ in resource use to avoid competitive exclusion. We identified 81 distinct arthropod taxa from fecal samples, belonging to 71 families representing 13 orders, which were predominantly from 16 dipteran, 13 lepidopteran, and 10 coleopteran families. Of all the prey taxa consumed, 45% were found to be distinct across the 10 babbler species, and ˂35% were shared simultaneously by ≥3 babbler species, indicating minimal dietary overlap. The black-throated babbler Stachyris nigricollis and moustached babbler Malacopteron magnirostre had the most generalist tendencies because they consumed a greater variety of prey taxa. Small dietary overlap values (Ojk) and a relatively wide range of food resources suggest that dietary segregation occurred among the studied babblers. The great diversity of prey consumed revealed the presence of dietary flexibility among the sympatric insectivorous birds, thus reducing any active dietary competition and facilitating the coexistence through niche partitioning.     

Phylogenetics of tribe Orchideae (Orchidaceae: Orchidoideae) based on combined DNA matrices: inferences regarding timing of diversification and evolution of pollination syndromes

Background and aims

Tribe Orchideae (Orchidaceae: Orchidoideae) comprises around 62 mostly terrestrial genera, which are well represented in the Northern Temperate Zone and less frequently in tropical areas of both the Old and New Worlds. Phylogenetic relationships within this tribe have been studied previously using only nuclear ribosomal DNA (nuclear ribosomal internal transcribed spacer, nrITS). However, different parts of the phylogenetic tree in these analyses were weakly supported, and integrating information from different plant genomes is clearly necessary in orchids, where reticulate evolution events are putatively common. The aims of this study were to: (1) obtain a well-supported and dated phylogenetic hypothesis for tribe Orchideae, (ii) assess appropriateness of recent nomenclatural changes in this tribe in the last decade, (3) detect possible examples of reticulate evolution and (4) analyse in a temporal context evolutionary trends for subtribe Orchidinae with special emphasis on pollination systems.

Methods

The analyses included 118 samples, belonging to 103 species and 25 genera, for three DNA regions (nrITS, mitochondrial cox1 intron and plastid rpl16 intron). Bayesian and maximum-parsimony methods were used to construct a well-supported and dated tree. Evolutionary trends in the subtribe were analysed using Bayesian and maximum-likelihood methods of character evolution.

Key Results

The dated phylogenetic tree strongly supported the recently recircumscribed generic concepts of Bateman and collaborators. Moreover, it was found that Orchidinae have diversified in the Mediterranean basin during the last 15 million years, and one potential example of reticulate evolution in the subtribe was identified. In Orchidinae, pollination systems have shifted on numerous occasions during the last 23 million years.

Conclusions

The results indicate that ancestral Orchidinae were hymenopteran-pollinated, food-deceptive plants and that these traits have been dominant throughout the evolutionary history of the subtribe in the Mediterranean. Evidence was also obtained that the onset of sexual deception might be linked to an increase in labellum size, and the possibility is discussed that diversification in Orchidinae developed in parallel with diversification of bees and wasps from the Miocene onwards.     

The modified castor bean catalase intron is incompletely spliced in tobacco and Arabidopsis

In an attempt to insert the modified castor bean catalase intron (mCBC intron) into the coding sequence of the Cre recombinase gene, we found that the mCBC intron was not completely spliced from the resulting iCre gene in tobacco and Arabidopsis. Sequencing and allele-specific PCR analyses indicated that six nucleotides (UUACAG) at the 3′ terminus of the mCBC intron were retained in the mature mRNA of the iCre gene. Moreover, the mCBC intron was incompletely spliced from the Gus gene in pCAMBIA vectors. A mutational analysis of the mCBC intron demonstrated that the incomplete splicing was due to an artificial 3′ splice site introduced by the insertion of an adenine, which created a TAG (stop) codon near the 3′ splice site of the original CBC intron. Deletion of the inserted adenine or the six nucleotides that were retained from the mCBC intron led to the complete removal of the intron from the resulting iCre2 and iCre3 genes. Thus, in this study, we not only characterized the incomplete splicing event of the mCBC intron in tobacco and Arabidopsis, but also reported the construction of two intron-containing Cre recombinase genes that are useful for plant biotechnology applications.     

Polymorphisms in FTO and near TMEM18 associate with type 2 diabetes and predispose to younger age at diagnosis of diabetes

Variations in the FTO gene and near the TMEM18 gene are risk factors for common form of obesity, but have also been linked with type 2 diabetes (T2D). Our aim was to investigate the contribution of these variants to risk of T2D in a population in Latvia. Four single nucleotide polymorphisms (SNP) in the first and fourth intronic regions of FTO and one close to TMEM18 were genotyped in 987 patients with T2D and 1080 controls selected from the Latvian Genome Data Base (LGDB). We confirmed association of SNPs in the first intron (rs11642015, rs62048402 and rs9939609) of FTO and rs7561317 representing the TMEM18 locus with T2D. Association between SNP in FTO and T2D remained significant after correction for body mass index (BMI). The rs57103849 located in the fourth intron of FTO and rs7561317 in TMEM18 showed BMI independent association with younger age at diagnosis of T2D. Our results add to the evidence that BMI related variants in and near FTO and TMEM18 may increase the risk for T2D not only through secondary effects of obesity. The influence of variants in the fourth intron of the FTO gene on development of T2D may be mediated by mechanisms other than those manifested by SNPs in the first intron of the same gene.     

Mutation bias is the driving force of codon usage in the Gallus gallus genome

Synonymous codons are used with different frequencies both among species and among genes within the same genome and are controlled by neutral processes (such as mutation and drift) as well as by selection. Up to now, a systematic examination of the codon usage for the chicken genome has not been performed. Here, we carried out a whole genome analysis of the chicken genome by the use of the relative synonymous codon usage (RSCU) method and identified 11 putative optimal codons, all of them ending with uracil (U), which is significantly departing from the pattern observed in other eukaryotes. Optimal codons in the chicken genome are most likely the ones corresponding to highly expressed transfer RNA (tRNAs) or tRNA gene copy numbers in the cell. Codon bias, measured as the frequency of optimal codons (Fop), is negatively correlated with the G + C content, recombination rate, but positively correlated with gene expression, protein length, gene length and intron length. The positive correlation between codon bias and protein, gene and intron length is quite different from other multi-cellular organism, as this trend has been only found in unicellular organisms. Our data displayed that regional G + C content explains a large proportion of the variance of codon bias in chicken. Stepwise selection model analyses indicate that G + C content of coding sequence is the most important factor for codon bias. It appears that variation in the G + C content of CDSs accounts for over 60% of the variation of codon bias. This study suggests that both mutation bias and selection contribute to codon bias. However, mutation bias is the driving force of the codon usage in the Gallus gallus genome. Our data also provide evidence that the negative correlation between codon bias and recombination rates in G. gallus is determined mostly by recombination-dependent mutational patterns.     

Group II intron folding under near-physiological conditions: collapsing to the near-native state

The folding of group II intron ribozymes has been studied extensively under optimal conditions for self-splicing in vitro (42 degrees C and high magnesium ion concentrations). In these cases, the ribozymes fold directly to the native state by an apparent two-state mechanism involving the formation of an obligate intermediate within intron domain 1. We have now characterized the folding pathway under near-physiological conditions. We observe that compaction of the RNA proceeds slowly to completion, even at low magnesium concentration (3 mM). Kinetic analysis shows that this compact species is a "near-native" intermediate state that is readily chased into the native state by the addition of high salt. Structural probing reveals that the near-native state represents a compact domain 1 scaffold that is not yet docked with the catalytic domains (D3 and D5). Interestingly, native ribozyme reverts to the near-native state upon reduction in magnesium concentration. Therefore, while the intron can sustain the intermediate state under physiological conditions, the native structure is not maintained and is likely to require stabilization by protein cofactors in vivo.     

A Megaraptor-like theropod (Dinosauria: Tetanurae) in Australia: support for faunal exchange across eastern and western Gondwana in the Mid-Cretaceous

The fossil record of Australian dinosaurs in general, and theropods in particular, is extremely sparse. Here we describe an ulna from the Early Cretaceous Eumeralla Formation of Australia that shares unique autapomorphies with the South American theropod Megaraptor. We also present evidence for the spinosauroid affinities of Megaraptor. This ulna represents the first Australian non-avian theropod with unquestionable affinities to taxa from other Gondwanan landmasses, suggesting faunal interchange between eastern and western Gondwana during the Mid-Cretaceous. This evidence counters claims of Laurasian affinities for Early Cretaceous Australian dinosaur faunas, and for the existence of a geographical or climatic barrier isolating Australia from the other Gondwanan continents during this time. The temporal and geographical distribution of Megaraptor and the Eumeralla ulna is also inconsistent with traditional palaeogeographic models for the fragmentation of Gondwana, but compatible with several alternative models positing connections between South America and Antarctica in the Mid-Cretaceous.     

Spliceosomal snRNAs in the unicellular eukaryote Trichomonas vaginalis are structurally conserved but lack a 5'-cap structure

Few genes in the divergent eukaryote Trichomonas vaginalis have introns, despite the unusually large gene repertoire of this human-infective parasite. These introns are characterized by extended conserved regulatory motifs at the 5' and 3' boundaries, a feature shared with another divergent eukaryote, Giardia lamblia, but not with metazoan introns. This unusual characteristic of T. vaginalis introns led us to examine spliceosomal small nuclear RNAs (snRNAs) predicted to mediate splicing reactions via interaction with intron motifs. Here we identify T. vaginalis U1, U2, U4, U5, and U6 snRNAs, present predictions of their secondary structures, and provide evidence for interaction between the U2/U6 snRNA complex and a T. vaginalis intron. Structural models predict that T. vaginalis snRNAs contain conserved sequences and motifs similar to those found in other examined eukaryotes. These data indicate that mechanisms of intron recognition as well as coordination of the two catalytic steps of splicing have been conserved throughout eukaryotic evolution. Unexpectedly, we found that T. vaginalis spliceosomal snRNAs lack the 5' trimethylguanosine cap typical of snRNAs and appear to possess unmodified 5' ends. Despite the lack of a cap structure, U1, U2, U4, and U5 genes are transcribed by RNA polymerase II, whereas the U6 gene is transcribed by RNA polymerase III.     

Molecular and functional dissection of a putative RNA-binding region in yeast mitochondrial leucyl-tRNA synthetase

Aminoacylation and editing by leucyl-tRNA synthetases (LeuRS) require migration of the tRNA acceptor stem end between the canonical aminoacylation core and a separate domain called CP1 that is responsible for amino acid editing. The LeuRS CP1 domain can also support group I intron RNA splicing in the yeast mitochondria, although splicing-sensitive sites have been identified on the main body. The RDW peptide, a highly conserved peptide within an RDW-containing motif, resides near one of the beta-strand linkers that connects the main body to the CP1 domain. We hypothesized that the RDW peptide was important for interactions of one or more of the LeuRS-RNA complexes. An assortment of X-ray crystallography structures suggests that the RDW peptide is dynamic and forms unique sets of interactions with the aminoacylation and editing complexes. Mutational analysis identified specific sites within the RDW peptide that failed to support protein synthesis activity in complementation experiments. In vitro enzymatic investigations of mutations at Trp445, Arg449, and Arg451 in yeast mitochondrial LeuRS suggested that these sites within the RDW peptide are critical to the aminoacylation complex, but impacted amino acid editing activity to a much less extent. We propose that these highly conserved sites primarily influence productive tRNA interactions in the aminoacylation complex.