Selective Enrichment and Sequencing of Whole Mitochondrial Genomes in the Presence of Nuclear Encoded Mitochondrial Pseudogenes (Numts)

Numts are an integral component of many eukaryote genomes offering a snapshot of the evolutionary process that led from the incorporation of an α-proteobacterium into a larger eukaryotic cell some 1.8 billion years ago. Although numt sequence can be harnessed as molecular marker, these sequences often remain unidentified and are mistaken for genuine mtDNA leading to erroneous interpretation of mtDNA data sets. It is therefore indispensable that during the process of amplifying and sequencing mitochondrial genes, preventive measures are taken to ensure the exclusion of numts to guarantee the recovery of genuine mtDNA. This applies to mtDNA analyses in general but especially to studies where mtDNAs are sequenced de novo as the launch pad for subsequent mtDNA-based research. By using a combination of dilution series and nested rolling circle amplification (RCA), we present a novel strategy to selectively amplify mtDNA and exclude the amplification of numt sequence. We have successfully applied this strategy to de novo sequence the mtDNA of the Black Field Cricket Teleogryllus commodus, a species known to contain numts. Aligning our assembled sequence to the reference genome of Teleogryllus emma (GenBank EU557269.1) led to the identification of a numt sequence in the reference sequence. This unexpected result further highlights the need of a reliable and accessible strategy to eliminate this source of error

Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons

BACKGROUND: Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA) sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus) using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining) depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. CONCLUSIONS/SIGNIFICANCE: Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b) as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species

Conservatism and adaptability during squirrel radiation : what is mandible shape telling us?

SYNTHESYS Project from the European Community Research Infrastructure (NL-TAF-4084)Both functional adaptation and phylogeny shape the morphology of taxa within clades. Herein we explore these two factors in an integrated way by analyzing shape and size variation in the mandible of extant squirrels using landmark-based geometric morphometrics in combination with a comparative phylogenetic analysis. Dietary specialization and locomotion were found to be reliable predictors of mandible shape, with the prediction by locomotion probably reflecting the underlying diet. In addition a weak but significant allometric effect could be demonstrated. Our results found a strong phylogenetic signal in the family as a whole as well as in the main clades, which is in agreement with the general notion of squirrels being a conservative group. This fact does not preclude functional explanations for mandible shape, but rather indicates that ancient adaptations kept a prominent role, with most genera having diverged little from their ancestral clade morphologies. Nevertheless, certain groups have evolved conspicuous adaptations that allow them to specialize on unique dietary resources. Such adaptations mostly occurred in the Callosciurinae and probably reflect their radiation into the numerous ecological niches of the tropical and subtropical forests of Southeastern Asia. Our dietary reconstruction for the oldest known fossil squirrels (Eocene, 36 million years ago) show a specialization on nuts and seeds, implying that the development from protrogomorphous to sciuromorphous skulls was not necessarily related to a change in diet

Data from: Evolution of Acoustic and Visual Signals in Asian Barbets

The study of animal communication systems is an important step towards gaining greater understanding of the processes influencing diversification because signals often play an important role in mate choice and can lead to reproductive isolation. Signal evolution can be influenced by a diversity of factors such as biophysical constraints on the emitter, the signalling environment, or selection to avoid heterospecific matings. Furthermore, because signals can be costly to produce, trade-offs may exist between different types of signals. Here, we apply phylogenetic comparative analyses to study the evolution of acoustic and visual signals in Asian barbets, a clade of non-Passerine, forest-dependent birds. Our results suggest that evolution of acoustic and visual signals in barbets is influenced by diverse factors, such as morphology and signalling environment, suggesting a potential effect of sensory drive. We found no trade-offs between visual and acoustic signals. Quite to the contrary, more colourful species sing significantly longer songs. Song characteristics presented distinct patterns of evolution. Song frequency diverged early on and the rate of evolution of this trait appears to be constrained by body size. On the other hand, characteristics associated with length of the song presented evidence for more recent divergence. Finally, our results indicate that there is a spatial component to the evolution of visual signals, and that visual signals are more divergent between closely related taxa than acoustic signals. Hence, visual signals in these species could play a role in speciation or reinforcement of reproductive isolation following secondary contacts

Assessment of foot deformities in individuals with cerebral palsy using weight-bearing CT

Objective: The aims of this study were to visualize and quantify relative bone positions in the feet of individuals with cerebral palsy (CP) with a foot deformity and compare bone positions with those of typically developed (TD) controls. Materials and methods: Weight-bearing CT images of 14 individuals with CP scheduled for tendon transfer and/or bony surgery and of 20 TD controls were acquired on a Planmed Verity WBCT scanner. Centroids of the navicular and calcaneus with respect to the talus were used to quantify foot deformities. All taluses were aligned and the size and dimensions of the individuals’ talus were scaled to correct for differences in bone sizes. In order to visualize and quantify variations in relative bone positions, 95% CI ellipsoids and standard deviations in its principle X-, Y-, and Z-directions were determined. Results: In individuals with CP (age 11–17), a large variation in centroid positions was observed compared to data of TD controls. Radiuses of the ellipsoids, representing the standard deviations of the 95% CI in the principle X-, Y-, and Z-directions, were larger in individuals with CP compared to TD controls for both the calcaneus (3.16 vs 1.86 mm, 4.26 vs 2.60 mm, 9.19 vs 3.60 mm) and navicular (4.63 vs 1.55 mm, 5.18 vs 2.10 mm, 16.07 vs 4.16 mm). Conclusion: By determining centroids of the calcaneus and navicular with respect to the talus on WBCT images, normal and abnormal relative bone positions can be visualized and quantified in individuals with CP with various foot deformities

Assessment of foot deformities in individuals with cerebral palsy using weight-bearing CT

Objective: The aims of this study were to visualize and quantify relative bone positions in the feet of individuals with cerebral palsy (CP) with a foot deformity and compare bone positions with those of typically developed (TD) controls. Materials and methods: Weight-bearing CT images of 14 individuals with CP scheduled for tendon transfer and/or bony surgery and of 20 TD controls were acquired on a Planmed Verity WBCT scanner. Centroids of the navicular and calcaneus with respect to the talus were used to quantify foot deformities. All taluses were aligned and the size and dimensions of the individuals’ talus were scaled to correct for differences in bone sizes. In order to visualize and quantify variations in relative bone positions, 95% CI ellipsoids and standard deviations in its principle X-, Y-, and Z-directions were determined. Results: In individuals with CP (age 11–17), a large variation in centroid positions was observed compared to data of TD controls. Radiuses of the ellipsoids, representing the standard deviations of the 95% CI in the principle X-, Y-, and Z-directions, were larger in individuals with CP compared to TD controls for both the calcaneus (3.16 vs 1.86 mm, 4.26 vs 2.60 mm, 9.19 vs 3.60 mm) and navicular (4.63 vs 1.55 mm, 5.18 vs 2.10 mm, 16.07 vs 4.16 mm). Conclusion: By determining centroids of the calcaneus and navicular with respect to the talus on WBCT images, normal and abnormal relative bone positions can be visualized and quantified in individuals with CP with various foot deformities