Multigene phylogeny of the Mustelidae: Resolving relationships, tempo and biogeographic history of a mammalian adaptive radiation

<p>Abstract</p> <p>Background</p> <p>Adaptive radiation, the evolution of ecological and phenotypic diversity from a common ancestor, is a central concept in evolutionary biology and characterizes the evolutionary histories of many groups of organisms. One such group is the Mustelidae, the most species-rich family within the mammalian order Carnivora, encompassing 59 species classified into 22 genera. Extant mustelids display extensive ecomorphological diversity, with different lineages having evolved into an array of adaptive zones, from fossorial badgers to semi-aquatic otters. Mustelids are also widely distributed, with multiple genera found on different continents. As with other groups that have undergone adaptive radiation, resolving the phylogenetic history of mustelids presents a number of challenges because ecomorphological convergence may potentially confound morphologically based phylogenetic inferences, and because adaptive radiations often include one or more periods of rapid cladogenesis that require a large amount of data to resolve.</p> <p>Results</p> <p>We constructed a nearly complete generic-level phylogeny of the Mustelidae using a data matrix comprising 22 gene segments (~12,000 base pairs) analyzed with maximum parsimony, maximum likelihood and Bayesian inference methods. We show that mustelids are consistently resolved with high nodal support into four major clades and three monotypic lineages. Using Bayesian dating techniques, we provide evidence that mustelids underwent two bursts of diversification that coincide with major paleoenvironmental and biotic changes that occurred during the Neogene and correspond with similar bursts of cladogenesis in other vertebrate groups. Biogeographical analyses indicate that most of the extant diversity of mustelids originated in Eurasia and mustelids have colonized Africa, North America and South America on multiple occasions.</p> <p>Conclusion</p> <p>Combined with information from the fossil record, our phylogenetic and dating analyses suggest that mustelid diversification may have been spurred by a combination of faunal turnover events and diversification at lower trophic levels, ultimately caused by climatically driven environmental changes. Our biogeographic analyses show Eurasia as the center of origin of mustelid diversity and that mustelids in Africa, North America and South America have been assembled over time largely via dispersal, which has important implications for understanding the ecology of mustelid communities.</p

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. METHODS: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. RESULTS: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. CONCLUSIONS: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation

Phenotypic Characterization of <i>EIF2AK4</i> Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension

Background: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 ( BMPR2 ) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene ( EIF2AK4 ) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. Methods: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource–Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of &lt;1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. Results: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (K co ; 33% [interquartile range, 30%–35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23–38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. Conclusions: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low K co and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation. </jats:sec

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper

A Reference-less Injection-Locked Clock Recovery Scheme for Multilevel-Signaling-Based Wideband BCC Receivers

Subject: Engineering, Electrical & ElectronicBody channel communication (BCC) integrated circuits for emerging wireless body area network multimedia applications call for the need of high-speed inter-device data communication at ultra-low-power consumption and smaller device footprint. In this paper, a novel low-power injection-locking-based clock-recovery circuit (CRC) is proposed for BCC transceivers that employ multilevel direct digital signaling for high data rates. The CRC utilizes transition detection for generating pulses from transmitted digital data and injects them directly into the VCO to recover the clock. The pulse-based direct injection-locking architecture achieves instantaneous clock recovery from random multilevel data with a sensitivity of up to -43 dBm, and eliminates the need for a reference crystal used in conventional phase-locked-loop-based CRC circuits. Measured results verify that the proposed CRC achieves clock recovery for two-and three-level signals for data rates up to 160 Mb/s. Implemented in 65-nm CMOS technology, the CRC consumes 0.84 mW with a footprint of 0.12 mm(2).Agency for Science, Technology and Research (A*STAR), Science and Engineering Research Council (SERC), Singapore under NeuroDevices Progra

Vascularized fibular graft in infected tibial bone loss

Background : The treatment options of bone loss with infections include bone transport with external fixators, vascularized bone grafts, non-vascularized autogenous grafts and vascularized allografts. The research hypothesis was that the graft length and intact ipsilateral fibula influenced hypertrophy and stress fracture. We retrospectively studied the graft hypertrophy in 15 patients, in whom vascularized fibular graft was done for post-traumatic tibial defects with infection. Materials and Methods : 15 male patients with mean age 33.7 years (range 18 - 56 years) of post traumatic tibial bone loss were analysed. The mean bony defect was 14.5 cm (range 6.5 - 20 cm). The mean length of the graft was 16.7 cm (range 11.5 - 21 cm). The osteoseptocutaneous flap (bone flap with attached overlying skin flap) from the contralateral side was used in all patients except one. The graft was fixed to the recipient bone at both ends by one or two AO cortical screws, supplemented by a monolateral external fixator. A standard postoperative protocol was followed in all patients. The hypertrophy percentage of the vascularized fibular graft was calculated by a modification of the formula described by El-Gammal. The followup period averaged 46.5 months (range 24 - 164 months). The Pearson correlation coefficient (r) was worked out, to find the relationship between graft length and hypertrophy. The t-test was performed to find out if there was any significant difference in the graft length of those who had a stress fracture and those who did not and to find out whether there was any significant difference in hypertrophy with and without ipsilateral fibula union. The Chi square test was performed to identify whether there was any association between the stress fracture and the fibula union. Given the small sample size we have not used any statistical analysis to determine the relation between the percentage of the graft hypertrophy and stress fracture. Results : Graft union occurred in all patients in a mean time of 3.3 months, at both ends. At a minimum followup of 24 months the mean hypertrophy noted was 63.6% (30 - 136%) in the vascularized fibular graft. Ten stress fractures occurred in seven patients. The mean duration of the occurrence of a stress fracture in the graft was 11.1 months (2.5 - 18 months) postoperatively. The highest incidence of stress fractures was when the graft hypertrophy was less than 20%. The incidence of stress fractures reduced significantly after the graft hypertrophy exceeded 20%. Conclusion : In most cases hypertrophy of the vascularized fibular graft occurs in response to mechanical loading by protected weight bearing, and the amount of hypertrophy is variable. The presence or absence of an intact fibula has no bearing on the hypertrophy or incidence of stress fracture. The length of the fibular graft has no bearing on the hypertrophy or stress fracture