Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci collected across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g., exons). However, molecular techniques requiring RNA as a template are limited to using very high quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n$=$1510) of ultraconserved elements (UCE) shared among the insect order Hymenoptera. We use in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled Hymenoptera, and we design a set of baits for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We use our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we use these UCE loci to reconstruct phylogenetic relationships spanning very old ($\geq$220 MYA) to very young ($\leq$1 MYA) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support

A MULTI‐GENE ESTIMATE OF HIGHER‐LEVEL PHYLOGENETIC RELATIONSHIPS AMONG NIGHTJARS (AVES: CAPRIMULGIDAE)

ABSTRACT ∙ The higher‐level phylogenetic relationships of the nightjars and nighthawks (Caprimulgidae) have been challenging for traditional systematics due to their cryptic plumage and conservative morphology. We explored these relationships by combining two previously published molecular datasets with new data to generate a complete matrix (7,104 bp) of evolutionarily disparate sequence elements from four genes for 36 taxa. We analyzed each of the genes separately for base composition heterogeneity and heterozygosity. We analyzed the concatenated matrix in a likelihood framework using seven different partitioning schemes. As the number of subsets in a given partitioning scheme increased, tree length and likelihood score also increased; however, the branching topology was little affected by increasingly complex partitioning schemes. Our best maximum likelihood tree has increased bootstrap support at 13 of 30 ingroup nodes compared with previous analyses, a result likely due to doubling the length of the sequence data. Coalescent‐based species tree inference produced a tree congruent with all strongly supported nodes in the maximum likelihood tree. This topology agrees with previous molecular studies in identifying three small, early branching Old World genera (Eurostopodus, Lyncornis, and Gactornis) and four more speciose terminal clades, representing the New World nighthawks (genus Chordeiles) and three nightjar radiations centered in South America, Central America and the Old World, respectively. Increased node support across the tree reinforces a historical scenario with origins in the region surrounding the Indian Ocean, followed by diversification in the New World and subsequent recolonization and radiation in the Old World. Future work on this group should incorporate additional members of the genera Lyncornis and Eurostopodus, to determine which is the basal lineage of Caprimulgidae.RESUMEN ∙ Relaciones filogenéticas de más alto nivel de los atajacaminos (Aves: Caprimulgidae) en base a un análisis multigénico Las relaciones filogenéticas de más alto nivel de los atajacaminos y añaperos (Caprimulgidae) son un reto para la sistemática tradicional, debido a que el grupo posee morfología poco variable y plumajes crípticos. Exploramos relaciones filogenéticas en el grupo combinando dos conjuntos de datos moleculares ya publicados con nuevos datos. La matriz completa (7,104 bp) se generó con cuatro genes y 36 taxones, incluyendo marcadores con distintos modelos de evolución. Se examinó cada uno de los genes por separado para determinar heterocigosidad y heterogeneidad de la composición de bases. Se analizó la matriz concatenada en un marco de máxima verosimilitud utilizando siete particiones diferentes. La longitud de los árboles filogenéticos y su verosimilitud aumentaron a la par del número de subconjuntos en una partición particular; sin embargo, la topología del árbol varió poco entre particiones. En comparación con topologías publicadas, nuestro árbol de máxima verosimilitud tuvo mejor soporte para 13 de los 30 nodos internos, resultado que podría deberse al uso del doble de los datos de secuencias. El método de árboles de especies basado en coalescencia produjo una topología congruente con la obtenida por máxima verosimilitud. Esta topología concuerda con previos estudios moleculares, identificando tres pequeños géneros del Viejo Mundo como basales en la filogenia (Eurostopodus, Lyncornis y Gactornis), y cuatro clados terminales con más especies. Estos clados terminales representan los atajacaminos del Nuevo Mundo del género Chordeiles, y otras tres radiaciones de América del Sur, Central y del Viejo Mundo. Nuestros resultados sugieren un escenario histórico con orígenes del grupo en la región circundante al Océano Indico, seguido por la diversificación en las Américas y la posterior recolonización y radiación en el Viejo Mundo. Futuros estudios en este grupo deben incorporar miembros adicionales de los géneros Lyncornis y Eurostopodus, lo que permitirá estudiar cuál es el linaje basal de Caprimulgidae

Overcoming Redundancy: An RNAi Enhancer Screen for Morphogenesis Genes in Caenorhabditis elegans

Morphogenesis is an important component of animal development. Genetic redundancy has been proposed to be common among morphogenesis genes, posing a challenge to the genetic dissection of morphogenesis mechanisms. Genetic redundancy is more generally a challenge in biology, as large proportions of the genes in diverse organisms have no apparent loss of function phenotypes. Here, we present a screen designed to uncover redundant and partially redundant genes that function in an example of morphogenesis, gastrulation in Caenorhabditis elegans. We performed an RNA interference (RNAi) enhancer screen in a gastrulation-sensitized double-mutant background, targeting genes likely to be expressed in gastrulating cells or their neighbors. Secondary screening identified 16 new genes whose functions contribute to normal gastrulation in a nonsensitized background. We observed that for most new genes found, the closest known homologs were multiple other C. elegans genes, suggesting that some may have derived from rounds of recent gene duplication events. We predict that such genes are more likely than single copy genes to comprise redundant or partially redundant gene families. We explored this prediction for one gene that we identified and confirmed that this gene and five close relatives, which encode predicted substrate recognition subunits (SRSs) for a CUL-2 ubiquitin ligase, do indeed function partially redundantly with each other in gastrulation. Our results implicate new genes in C. elegans gastrulation, and they show that an RNAi-based enhancer screen in C. elegans can be used as an efficient means to identify important but redundant or partially redundant developmental genes

How and Why Chromosome Inversions Evolve

Chromosome inversions are a major engine of genome evolution. New genomic and ecological data are beginning to reveal the evolutionary forces that drive the evolution of inversions

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1)

The cost of uncomplicated childhood fevers to Kenyan households: implications for reaching international access targets

BACKGROUND: Fever is the clinical hallmark of malaria disease. The Roll Back Malaria (RBM) movement promotes prompt, effective treatment of childhood fevers as a key component to achieving its optimistic mortality reduction goals by 2010. A neglected concern is how communities will access these new medicines promptly and the costs to poor households when they are located in rural areas distant to health services. METHODS: We assemble data developed between 2001 and 2002 in Kenya to describe treatment choices made by rural households to treat a child's fever and the related costs to households. Using a cost-of-illness approach, we estimate the expected cost of a childhood fever to Kenyan households in 2002. We develop two scenarios to explore how expected costs to households would change if more children were treated at a health care facility with an effective antimalarial within 48 hours of fever onset. RESULTS: 30% of uncomplicated fevers were managed at home with modern medicines, 38% were taken to a health care facility (HCF), and 32% were managed at home without the use of modern medicines. Direct household cash expenditures were estimated at $0.44 per fever, while the total expected cost to households (cash and time) of an uncomplicated childhood fever is estimated to be$1.91. An estimated mean of 1.42 days of caretaker time devoted to each fever accounts for the majority of household costs of managing fevers. The aggregate cost to Kenyan households of managing uncomplicated childhood fevers was at least $96 million in 2002, equivalent to 1.00$1.86 because caretakers also save time with prompt treatment if the child has malaria. CONCLUSION: The management of uncomplicated childhood fevers imposes substantial costs on Kenyan households. Achieving substantial improvements in the numbers of fevers treated within 48 hours at a HCF with an effective antimalarial drug (Scenario 1) will not impose additional costs on households. Achieving additional improvements in fevers treated promptly at a HCF (Scenario 2) will impose additional costs on some households roughly equal to average cash expenses for transportation to a HCF. Additional financing mechanisms that further reduce the costs of accessing care at a HCF and/or that make artemisinin-based combination therapies (ACTs) accessible for home management need to be developed and evaluated as a top priority

Gene Expression Disruptions of Organism versus Organ in Drosophila Species Hybrids

Hybrid dysfunctions, such as sterility, may result in part from disruptions in the regulation of gene expression. Studies of hybrids within the Drosophila simulans clade have reported genes expressed above or below the expression observed in their parent species, and such misexpression is associated with male sterility in multigenerational backcross hybrids. However, these studies often examined whole bodies rather than testes or had limited replication using less-sensitive but global techniques. Here, we use a new RNA isolation technique to re-examine hybrid gene expression disruptions in both testes and whole bodies from single Drosophila males by real-time quantitative RT-PCR. We find two early-spermatogenesis transcripts are underexpressed in hybrid whole-bodies but not in assays of testes alone, while two late-spermatogenesis transcripts seem to be underexpressed in both whole-bodies and testes alone. Although the number of transcripts surveyed is limited, these results provide some support for a previous hypothesis that the spermatogenesis pathway in these sterile hybrids may be disrupted sometime after the expression of the early meiotic arrest genes

Why don't health workers prescribe ACT? A qualitative study of factors affecting the prescription of artemether-lumefantrine

BACKGROUND: Kenya recently changed its antimalarial drug policy to a specific artemisinin-based combination therapy (ACT), artemether-lumefantrine (AL). New national guidelines on the diagnosis, treatment and prevention were developed and disseminated to health workers together with in-service training. METHODS: Between January and March 2007, 36 in-depth interviews were conducted in five rural districts with health workers who attended in-service training and were non-adherent to the new guidelines. A further 20 interviews were undertaken with training facilitators and members of District Health Management Teams (DHMTs) to explore reasons underlying health workers' non-adherence. RESULTS: Health workers generally perceived AL as being tolerable and efficacious as compared to amodiaquine and sulphadoxine-pyremethamine. However, a number of key reasons for non-adherence were identified. Insufficient supply of AL was a major issue and hence fears of stock outs and concern about AL costs was an impediment to AL prescription. Training messages that contradicted the recommended guidelines also led to health worker non-adherence, compounded by a lack of follow-up supervision. In addition, the availability of non-recommended antimalarials such as amodiaquine caused prescription confusion. Some health workers and DHMT members maintained that shortage of staff had resulted in increased patient caseload affecting the delivery of the desirable quality of care and adherence to guidelines. CONCLUSION: The introduction of free efficacious ACTs in the public health sector in Kenya and other countries has major potential public health benefits for Africa. These may not be realized if provider prescription practices do not conform to the recommended treatment guidelines. It is essential that high quality training, drug supply and supervision work synergistically to ensure appropriate case management

Utilisation of an operative difficulty grading scale for laparoscopic cholecystectomy

Background A reliable system for grading operative difficulty of laparoscopic cholecystectomy would standardise description of findings and reporting of outcomes. The aim of this study was to validate a difficulty grading system (Nassar scale), testing its applicability and consistency in two large prospective datasets. Methods Patient and disease-related variables and 30-day outcomes were identified in two prospective cholecystectomy databases: the multi-centre prospective cohort of 8820 patients from the recent CholeS Study and the single-surgeon series containing 4089 patients. Operative data and patient outcomes were correlated with Nassar operative difficultly scale, using Kendall’s tau for dichotomous variables, or Jonckheere–Terpstra tests for continuous variables. A ROC curve analysis was performed, to quantify the predictive accuracy of the scale for each outcome, with continuous outcomes dichotomised, prior to analysis. Results A higher operative difficulty grade was consistently associated with worse outcomes for the patients in both the reference and CholeS cohorts. The median length of stay increased from 0 to 4 days, and the 30-day complication rate from 7.6 to 24.4% as the difficulty grade increased from 1 to 4/5 (both p < 0.001). In the CholeS cohort, a higher difficulty grade was found to be most strongly associated with conversion to open and 30-day mortality (AUROC = 0.903, 0.822, respectively). On multivariable analysis, the Nassar operative difficultly scale was found to be a significant independent predictor of operative duration, conversion to open surgery, 30-day complications and 30-day reintervention (all p < 0.001). Conclusion We have shown that an operative difficulty scale can standardise the description of operative findings by multiple grades of surgeons to facilitate audit, training assessment and research. It provides a tool for reporting operative findings, disease severity and technical difficulty and can be utilised in future research to reliably compare outcomes according to case mix and intra-operative difficulty

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation

A set of experiments demonstrates the involvement of a chromosomal inversion in the adaptive transition between annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatu