Single-copy nuclear genes recover cretaceous-age divergences in bees

We analyzed the higher level phylogeny of the bee family Halictidae based on the coding regions of three single-copy nuclear genes (long-wavelength [LW] opsin, wingless, and elongation factor 1-alpha [EF-1 alpha]). Our combined data set consisted of 2,234 aligned nucleotide sites (702 base pairs [bp] for LW opsin, 405 bp for wingless, and 1,127 bp for EF-1 alpha) and 779 parsimony-informative sites. We included 58 species of halictid bees from 33 genera, representing all subfamilies and tribes, and rooted the trees using seven outgroups from other bee families: Colletidae, Andrenidae, Melittidae, and Apidae. We analyzed the separate and combined data sets by a variety of methods, including equal weights parsimony, maximum likelihood, and Bayesian methods. Analysis of the combined data set produced a strong phylogenetic signal with high bootstrap and Bremer support and high posterior probability well into the base of the tree. The phylogeny recovered the monophyly of the Halictidae and of all four subfamilies and both tribes, recovered relationships among the subfamilies and tribes congruent with morphology, and provided robust support for the relationships among the numerous genera in the tribe Halictini, sensu Michener (2000). Using our combined nucleotide data set, several recently described halictid fossils from the Oligocene and Eocene, and recently developed Bayesian methods, we estimated the antiquity of major clades within the family. Our results indicate that each of the four subfamilies arose well before the Cretaceous-Tertiary boundary and suggest that the early radiation of halictid bees involved substantial African-South American interchange roughly coincident with the separation of these two continents in the late Cretaceous. This combination of single-copy nuclear genes is capable of recovering Cretaceous-age divergences in bees with high levels of support. We propose that LW opsin, wingless, and EF-1 alpha(F2 copy) may be useful in resolving relationships among bee families and other Cretaceous-age insect lineages.     

18S rDNA sequences and the holometabolous insects

The Holometabola (insects with complete metamorphosis: beetles, wasps, flies, fleas, butterflies, lacewings, and others) is a monophyletic group that includes the majority of the world's animal species. Holometabolous orders are well defined by morphological characters, but relationships among orders are unclear. In a search for a region of DNA that will clarify the interordinal relationships we sequenced approximately 1080 nucleotides of the 5' end of the 18S ribosomal RNA gene from representatives of 14 families of insects in the orders Hymenoptera (sawflies and wasps), Neuroptera (lacewing and antlion), Siphonaptera (flea), and Mecoptera (scorpionfly). We aligned the sequences with the published sequences of insects from the orders Coleoptera (beetle) and Diptera (mosquito and Drosophila), and the outgroups aphid, shrimp, and spider. Unlike the other insects examined in this study, the neuropterans have A-T rich insertions or expansion regions: one in the antlion was approximately 260 bp long. The dipteran 18S rDNA evolved rapidly, with over 3 times as many substitutions among the aligned sequences, and 2-3 times more unalignable nucleotides than other Holometabola, in violation of an insect-wide molecular clock. When we excluded the long-branched taxa (Diptera, shrimp, and spider) from the analysis, the most parsimonious (minimum-length) trees placed the beetle basal to other holometabolous orders, and supported a morphologically monophyletic clade including the fleas+scorpionflies (96% bootstrap support). However, most interordinal relationships were not significantly supported when tested by maximum likelihood or bootstrapping and were sensitive to the taxa included in the analysis. The most parsimonious and maximum-likelihood trees both separated the Coleoptera and Neuroptera, but this separation was not statistically significant.(ABSTRACT TRUNCATED AT 250 WORDS)     

Common and distinct roles of juvenile hormone signaling genes in metamorphosis of holometabolous and hemimetabolous insects

Insect larvae metamorphose to winged and reproductive adults either directly (hemimetaboly) or through an intermediary pupal stage (holometaboly). In either case juvenile hormone (JH) prevents metamorphosis until a larva has attained an appropriate phase of development. In holometabolous insects, JH acts through its putative receptor Methoprene-tolerant (Met) to regulate Krüppel-homolog 1 (Kr-h1) and Broad-Complex (BR-C) genes. While Met and Kr-h1 prevent precocious metamorphosis in pre-final larval instars, BR-C specifies the pupal stage. How JH signaling operates in hemimetabolous insects is poorly understood. Here, we compare the function of Met, Kr-h1 and BR-C genes in the two types of insects. Using systemic RNAi in the hemimetabolous true bug, Pyrrhocoris apterus, we show that Met conveys the JH signal to prevent premature metamorphosis by maintaining high expression of Kr-h1. Knockdown of either Met or Kr-h1 (but not of BR-C) in penultimate-instar Pyrrhocoris larvae causes precocious development of adult color pattern, wings and genitalia. A natural fall of Kr-h1 expression in the last larval instar normally permits adult development, and treatment with an exogenous JH mimic methoprene at this time requires both Met and Kr-h1 to block the adult program and induce an extra larval instar. Met and Kr-h1 therefore serve as JH-dependent repressors of deleterious precocious metamorphic changes in both hemimetabolous and holometabolous juveniles, whereas BR-C has been recruited for a new role in specifying the holometabolous pupa. These results show that despite considerable evolutionary distance, insects with diverse developmental strategies employ a common-core JH signaling pathway to commit to adult morphogenesis.     

Combined analysis of fourteen nuclear genes refines the Ursidae phylogeny

Despite numerous studies, questions remain about the evolutionary history of Ursidae and additional independent genetic markers were needed to elucidate these ambiguities. For this purpose, we sequenced ten nuclear genes for all the eight extant bear species. By combining these new sequences with those of four other recently published nuclear markers, we provide new insights into the phylogenetic relationships of the Ursidae family members. The hypothesis that the giant panda was the first species to diverge among ursids is definitively confirmed and the precise branching order within the Ursus genus is clarified for the first time. Moreover, our analyses indicate that the American and the Asiatic black bears do not cluster as sister taxa, as had been previously hypothesised. Sun and sloth bears clearly appear as the most basal ursine species but uncertainties about their exact relationships remain. Since our larger dataset did not enable us to clarify this last question, identifying rare genomic changes in bear genomes could be a promising solution for further studies.     

Evolutionary contrasts in insects: nutritional advantages of holometabolous development

ABSTRACT. Two insects, one holometabolous and one hemimetabolous, are compared and contrasted in respect to feeding efficiency, growth and respiration. An examination of cuticle production in these and other species leads to the conclusion that the nutritional burden of cuticle production in hemimetabolous forms has a significant effect on efficiency, and it is speculated that greater nutritional efficiency in holometabolous forms has been an important evolutionary advantage.     

Snake phylogeny: evidence from nuclear and mitochondrial genes

We constructed phylogenies of snakes from the c-mos and cytochrome b genes using conventional phylogenetic methods as well as the relatively new method of Bayesian inference. For all methods, there was excellent congruence between the c-mos and cytochrome b genes, implying a high level of support for the shared clades. Our results agree with previous studies in two important respects: first, that the scolecophidians and alethinophidians are monophyletic sister clades; and second, that the Colubroidea is a monophyletic group with the Acrochordidae as its sister clade. However, our results differ from previous studies in the finding that Loxocemus and Xenopeltis cluster with pythons. An additional noteworthy result from our data is that the genera Exiliboa and Ungaliophis, often placed with Tropidophis (and Trachyboa, not included in the present study) in the Tropidophiidae, are in reality boids.     

Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes

Background  

Phylogenetic analyses of jawed vertebrates based on mitochondrial sequences often result in confusing inferences which are obviously inconsistent with generally accepted trees. In particular, in a hypothesis by Rasmussen and Arnason based on mitochondrial trees, cartilaginous fishes have a terminal position in a paraphyletic cluster of bony fishes. No previous analysis based on nuclear DNA-coded genes could significantly reject the mitochondrial trees of jawed vertebrates.     

A rapid methylene blue staining procedure for the ventral nerve cord of holometabolous insects

The author describes a modification of the methylene blue technique that stains neurons dark blue against a clear background. The resolution of the dendritic tree attains Golgi-like quality. The procedure offers a rapid, easily adaptable alternative to the reduced silver procedures in holometabolous insects.     

When insects help to resolve plant phylogeny: evidence for a paraphyletic genus Acacia from the systematics and host-plant range of their seed-predators

In this study we use an indirect method to address the issue of the systematics of the large and economically important genus Acacia (Leguminosae, Mimosoideae, Acacieae). We propose the use of host-preference data in closely related insect species as a potentially useful tool to investigate host systematic issues, especially when other approaches yield inconsistent results. We have examined the evolution of host-plant use of a highly specialized group of seed-feeders who predate Acacia — the seed-beetles (Coleoptera, Chrysomelidae, Bruchinae). First, the evolution of host-plant preferences in a large clade of Bruchidius species was investigated using molecular phylogenetics and character optimization methods. Second, the scope of our study was enlarged by critically reviewing the host-plant records of all bruchine genera associated with Acacia . Both morphological and molecular data were used to define relevant insect clades, for which comparisons of host-plant range were performed. Interestingly, the analyses of host-plant preferences from 163 seed-beetle species recovered similar patterns of host-plant associations in the distinct clades which develop within Acacia seeds. Our results clearly support the hypothesis of Acacia being a paraphyletic genus and provide useful insights with reference to the systematics of the whole subfamily as well. This study should also be of interest to those involved in the numerous biological control programs which either already use or aim to use seed-beetles as auxiliary species to limit the propagation of several invasive legume tree species.     

Near intron positions are reliable phylogenetic markers: an application to holometabolous insects

Today, the reconstruction of the organismal evolutionary tree is based mainly on molecular sequence data. However, sequence data are sometimes insufficient to reliably resolve in particular deep branches. Thus, it is highly desirable to find novel, more reliable types of phylogenetic markers that can be derived from the wealth of genomic data. Here, we consider the gain of introns close to older preexisting ones. Because correct splicing is impeded by very small exons, nearby pairs of introns very rarely coexist, that is, the gain of the new intron is nearly always associated with the loss of the old intron. Both events may even be directly connected as in cases of intron migration. Therefore, it should be possible to identify one of the introns as ancient (plesiomorphic) and the other as novel (derived or apomorphic). To test the suitability of such near intron pairs (NIPs) as a marker class for phylogenetic analysis, we undertook an analysis of the evolutionary positions of bees and wasps (Hymenoptera) and beetles (Coleoptera) in relation to moths (Lepidoptera) and dipterans (Diptera) using recently completed genome project data. By scanning 758 putatively orthologous gene structures of Apis mellifera (Hymenoptera) and Tribolium castaneum (Coleoptera), we identified 189 pairs of introns, one from each species, which are located less than 50 nt from each other. A comparison with genes from 5 other holometabolan and 9 metazoan outgroup genomes resulted in 22 shared derived intron positions found in beetle as well as in butterflies and/or dipterans. This strongly supports a basal position of hymenopterans in the holometabolous insect tree. In addition, we found 31 and 12 intron positions apomorphic for A. mellifera and T. castaneum, respectively, which seem to represent changes inside these branches. Another 12 intron pairs indicate parallel intron gains or extraordinarily small exons. In conclusion, we show here that the analysis of phylogenetically nested, nearby intron pairs is suitable to identify evolutionarily younger intron positions and to determine their relative age, which should be of equal importance for the understanding of intron evolution and the reconstruction of the eukaryotic tree.     

The evolution of developmental gene networks: lessons from comparative studies on holometabolous insects

Recent comparative studies have revealed significant differences in the developmental gene networks operating in three holometabolous insects: the beetle Tribolium castaneum, the parasitic wasp Nasonia vitripennis and the fruitfly Drosophila melanogaster. I discuss these differences in relation to divergent and convergent changes in cellular embryology. I speculate on how segmentation gene networks have evolved to operate in divergent embryological contexts, and highlight the role that co-option might have played in this process. I argue that insects represent an important example of how diversification in life-history strategies between lineages can lead to divergence in the genetic and cellular mechanisms controlling the development of homologous adult structures.     

Modularity, evolvability, and adaptive radiations: a comparison of the hemi- and holometabolous insects

SUMMARY Despite recent attention given to the concept of modularity and its potential contribution to the evolvability of organisms, there has been little mention of how such a contribution may affect rates of diversification or how this would be assessed. A first key prediction is that lineages with relatively greater degrees of modularity in given traits should exhibit higher rates of diversification. Four general conditions for testing this prediction of the modular evolvability hypothesis are outlined here. The potential role of modularity as a deterministic factor in adaptive radiations is best examined by looking at historic patterns of diversification rather than just levels of extant diversity, the focus of most analyses of key innovations.
Recent developmental evidence supports the notion that phenotypes of juvenile and adult stages of insects with "complete" metamorphosis (Holometabola) are distinct developmental and evolvable modules compared to the highly correlated life stages of insects with "incomplete" metamorphosis (Hemimetabola). Family-level rates of diversification for these two groups were calculated from the fossil record. The Holometabola was found to have a significantly and characteristically higher rate of diversification compared to the less modular Hemimetabola, consistent with the idea that intrinsic differences in modularity can influence the long-term evolvability of organisms.
The modular evolvability hypothesis also makes a second key prediction: that characters in more modular clades will exhibit greater levels of variation due to their independence. This provides an independent, phenotypically based test of the hypothesis. We discuss here how this second prediction may be tested in the case of the Hemi- and Holometabola.     

The phylogeny and classification of caenophidian snakes inferred from seven nuclear protein-coding genes

More than 80% of the approximately 3000 living species of snakes are placed in the taxon Caenophidia (advanced snakes), a group that includes the families Acrochordidae, Viperidae, Elapidae, Atractaspididae, and the paraphyletic 'Colubridae'. Previous studies using DNA sequences have involved few nuclear genes (one or two). Several nodes have therefore proven difficult to resolve with statistical significance. Here, we investigated the higher-level relationships of caenophidian snakes with seven nuclear protein-coding genes and obtained a well-supported topology. Accordingly, some adjustments to the current classification of Caenophidia are made to better reflect the relationships of the groups. The phylogeny also indicates that, ancestrally, caenophidian snakes are Asian and nocturnal in origin, although living species occur on nearly all continents and are ecologically diverse.     

Molecular phylogeny of silk-producing insects based on 16S ribosomal RNA and cytochrome oxidase subunit I genes

We have examined the molecular-phylogenetic relationships between nonmulberry and mulberry silkworm species that belong to the families Saturniidae, Bombycidae and Lasiocampidae using 16S ribosomal RNA (16S rRNA) and cytochrome oxidase subunit I (coxI) gene sequences. Aligned nucleotide sequences of 16S rRNA andcoxI from 14 silk-producing species were used for construction of phylogenetic trees by maximum likelihood and maximum parsimony methods. The tree topology on the basis of 16S rRNA supports monophyly for members of Saturniidae and Bombycidae. Weighted parsimony analysis weighted towards transversions relative to transitions (ts, tv4) forcoxI resulted in more robust bootstrap support over unweighted parsimony and favours the 16S rRNA tree topology. Combined analysis reflected clear biogeographic pattern, and agrees with morphological and cytological data.     

The mitochondrial genome of Bacillus stick insects (Phasmatodea) and the phylogeny of orthopteroid insects

The Order Phasmatodea (stick and leaf insects) includes many well-known species of cryptic phytophagous insects. In this work, we sequenced the almost complete mitochondrial genomes of two stick insect species of the genus Bacillus. Phasmatodea pertain to the Polyneoptera, and represent one of the major clades of heterometabolous insects. Orthopteroid insect lineages arose through rapid evolutionary radiation events, which likely blurred the phylogenetic reconstructions obtained so far; we therefore performed a phylogenetic analysis to resolve and date all major splits of orthopteroid phylogeny, including the relationships between Phasmatodea and other polyneopterans. We explored several molecular models, with special reference to data partitioning, to correctly detect any phylogenetic signal lying in rough data. Phylogenetic Informativeness analysis showed that the maximum resolving power on the orthopteroid mtDNA dataset is expected for the Upper Cretaceous, about 80millionyears ago (Mya), but at least 70% of the maximum informativeness is also expected for the 150-200 Mya timespan, which makes mtDNA a suitable marker to study orthopteroid splits. A complete chronological calibration has also been computed following a Penalized Likelihood method. In summary, our analysis confirmed the monophyly of Phasmatodea, Dictyoptera and Orthoptera, and retrieved Mantophasmatodea as sister group of Phasmatodea. The origin of orthopteroid insects was also estimated to be in the Middle Triassic, while the order Phasmatodea seems to appear in the Upper Jurassic. The obtained results evidenced that mtDNA is a suitable marker to unravel the ancient splits leading to the orthopteroid orders, given a proper methodological approach.     

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

Background

Bacterial biofilm is ubiquitous in nature. However, it is not clear how this crowded habitat would impact the evolution of bacteriophage (phage) life history traits. In this study, we constructed isogenic λ phage strains that only differed in their adsorption rates, because of the presence/absence of extra side tail fibers or improved tail fiber J, and maker states. The high cell density and viscosity of the biofilm environment was approximated by the standard double-layer agar plate. The phage infection cycle in the biofilm environment was decomposed into three stages: settlement on to the biofilm surface, production of phage progeny inside the biofilm, and emigration of phage progeny out of the current focus of infection.

Results

We found that in all cases high adsorption rate is beneficial for phage settlement, but detrimental to phage production (in terms of plaque size and productivity) and emigration out of the current plaque. Overall, the advantage of high adsorption accrued during settlement is more than offset by the disadvantages experienced during the production and emigration stages. The advantage of low adsorption rate was further demonstrated by the rapid emergence of low-adsorption mutant from a high-adsorption phage strain with the side tail fibers. DNA sequencing showed that 19 out of the 21 independent mutant clones have mutations in the stf gene, with the majority of them being single-nucleotide insertion/deletion mutations occurring in regions with homonucleotide runs.

Conclusion

We conclude that high mutation rate of the stf gene would ensure the existence of side tail fiber polymorphism, thus contributing to rapid adaptation of the phage population between diametrically different habitats of benthic biofilm and planktonic liquid culture. Such adaptability would also help to explain the maintenance of the stf gene in phage λ's genome.     

A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes

Even though the marsupial order Diprotodontia is one of the most heavily studied groups of Australasian marsupials, phylogenetic relationships within this group remain contentious. The more than 125 living species of Diprotodontia can be divided into two main groups: Vombatiformes (wombats and koalas) and Phalangerida. Phalangerida is composed of the kangaroos (Macropodidae, Potoroidae, and Hypsiprymnodontidae) and possums (Phalangeridae, Burramyidae, Petauridae, Pseudocheiridae, Tarsipedidae, and Acrobatidae). Much of the debate has focused on relationships among the families of possums and whether possums are monophyletic or paraphyletic. A limitation of previous investigations is that no study to date has investigated diprotodontian relationships using all genera. Here, we examine diprotodontian interrelationships using a nuclear multigene molecular data set representing all recognized extant diprotodontian genera. Maximum parsimony, maximum likelihood, and Bayesian methods were used to analyze sequence data obtained from protein-coding portions of ApoB, BRCA1, IRBP, Rag1, and vWF. We also applied a Bayesian relaxed molecular clock method to estimate times of divergence. Diprotodontia was rooted between Vombatiformes and Phalangerida. Within Phalangerida, the model-based methods strongly support possum paraphyly with Phalangeroidea (Burramyidae + Phalangeridae) grouping with the kangaroos (Macropodiformes) to the exclusion of Petauroidea (Tarsipedidae, Acrobatidae, Pseudocheiridae, and Petauridae). Within Petauroidea, Tarsipedidae grouped with both Petauridae and Pseudocheiridae to the exclusion of Acrobatidae. Our analyses also suggest that the diprotodontian genera Pseudochirops and Strigocuscus are paraphyletic and diphyletic, respectively, as currently recognized. Dating analyses suggest Diprotodontia diverged from other australidelphians in the late Paleocene to early Eocene with all interfamilial divergences occurring prior to the early Miocene except for the split between the Potoroidae and Macropodidae, which occurred sometime in the mid-Miocene. Ancestral state reconstructions using a Bayesian method suggest that the patagium evolved independently in the Acrobatidae, Petauridae, and Pseudocheiridae. Ancestral state reconstructions of ecological venue suggest that the ancestor of Diprotodontia was arboreal. Within Diprotodontia, the common ancestor of Macropodidae was reconstructed as terrestrial, suggesting that tree kangaroos (Dendrolagus) are secondarily arboreal.     

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

Background  

Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes.     

A preliminary phylogeny of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea) based on nuclear small-subunit ribosomal DNA

Scale insects (Hemiptera: Sternorrhyncha: Coccoidea) are a speciose and morphologically specialized group of plant-feeding bugs in which evolutionary relationships and thus higher classification are controversial. Sequences derived from nuclear small-subunit ribosomal DNA were used to generate a preliminary molecular phylogeny for the Coccoidea based on 39 species representing 14 putative families. Monophyly of the archaeococcoids (comprising Ortheziidae, Margarodidae sensu lato, and Phenacoleachia) was equivocal, whereas monophyly of the neococcoids was supported. Putoidae, represented by Puto yuccae, was found to be outside the remainder of the neococcoid clade. These data are consistent with a single origin (in the ancestor of the neococcoid clade) of a chromosome system involving paternal genome elimination in males. Pseudococcidae (mealybugs) appear to be sister to the rest of the neococcoids and there are indications that Coccidae (soft scales) and Kerriidae (lac scales) are sister taxa. The Eriococcidae (felt scales) was not recovered as a monophyletic group and the eriococcid genus Eriococcus sensu lato was polyphyletic.