THE VARIABLE GENOMIC ARCHITECTURE OF ISOLATION BETWEEN HYBRIDIZING SPECIES OF HOUSE MICE

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/1/EVO_846_sm_FigS3A.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/2/EVO_846_sm_legend.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/3/EVO_846_sm_FigS4.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/4/j.1558-5646.2009.00846.x.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/5/EVO_846_sm_FigS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/6/EVO_846_sm_FigS2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75350/7/EVO_846_sm_FigS3B.pd

Adaptation of the methotrexate in rheumatoid arthritis knowledge questionnaire (MiRAK) for use with parents of children with juvenile idiopathic arthritis (JIA)

Background: Although Methotrexate (MTX) is one of the most commonly prescribed disease-modifying drugs in JIA no questionnaire exists that assesses the knowledge of parents about this drug. A 60-item questionnaire was recently developed to measure rheumatoid arthritis (RA) patients’ knowledge about MTX; the Methotrexate in Rheumatoid Arthritis Knowledge Test (MiRAK; Ciciriello et al. (Arthritis Rheum 62:10–1009, 2010)). This study aimed to adapt the MiRAK for parents of children with JIA. Methods: Adaption of the MiRAK involved: 1) email consultations with clinicians working in the field of paediatric rheumatology (Panel 1) to ascertain the potential adaptations of the MiRAK from a clinical perspective, 2) synthesis of clinicians’ suggestions by a panel of experts, researchers and MiRAK developers (Panel 2) to reach consensus on which items needed to be modified and create a draft Methotrexate in Juvenile Idiopathic Arthritis Knowledge Test (MiJIAK), 3) a review of the draft by 5 parents of children with JIA (Panel 3) using the cognitive ‘think-aloud’ method, 4) a second consultation with Panel 2 to review parents’ suggestions and determine the final items. Results: A total of 9 items remained unchanged, e.g. “Methotrexate is effective at relieving joint stiffness”, 19 were deemed inappropriate in the paediatric setting and deleted, e.g. “It is safe to become pregnant 3 weeks after methotrexate has been stopped”, 32 underwent editorial changes largely to indicate that the questionnaire was about the children with JIA, e.g. “If you forget to give a dose of Methotrexate, you can still take it the next day” became “If your child misses a dose of Methotrexate, they can still take it the next day”, and 1 new item was added. A new 42-item questionnaire was produced and was found to be well understood by parents of children with JIA. Conclusions: The systematic modification of the MiRAK, a patient-centred MTX knowledge questionnaire, has generated a comprehensive new questionnaire for use in the JIA setting. The wide consultation process, including cognitive testing, has ensured the tool is both relevant and acceptable to clinicians and will therefore be a valuable addition in understanding the parents’ perspective of this treatment in JIA

Recent Hybrids Recapitulate Ancient Hybrid Outcomes

Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z chromosome in both the old and contemporary hybrids. The same pattern of reduced L. melissa ancestry on the Z chromosome is seen in two other ancient hybrid lineages. More generally, we find that patterns of ancestry in old or ancient hybrids are remarkably predictable from contemporary hybrids, which suggests selection and recombination affect hybrid genomes in a similar way across disparate time scales and during distinct stages of speciation and species breakdown

The genetic architecture of divergence between threespine stickleback species.

The genetic and molecular basis of morphological evolution is poorly understood, particularly in vertebrates. Genetic studies of the differences between naturally occurring vertebrate species have been limited by the expense and difficulty of raising large numbers of animals and the absence of molecular linkage maps for all but a handful of laboratory and domesticated animals. We have developed a genome-wide linkage map for the three-spined stickleback (Gasterosteus aculeatus), an extensively studied teleost fish that has undergone rapid divergence and speciation since the melting of glaciers 15,000 years ago. Here we use this map to analyse the genetic basis of recently evolved changes in skeletal armour and feeding morphologies seen in the benthic and limnetic stickleback species from Priest Lake, British Columbia. Substantial alterations in spine length, armour plate number, and gill raker number are controlled by genetic factors that map to independent chromosome regions. Further study of these regions will help to define the number and type of genetic changes that underlie morphological diversification during vertebrate evolution

The Impact of Response to MTX on the Illness and Treatment Beliefs of Parents of Children with JIA

Background: Research on adult patients with chronic illness has shown that their illness beliefs are associated with patient reported outcomes. There is limited research focusing on the illness and treatment beliefs of parents of ill children. The aim of this study was to discern if treatment success, as measured by the ACR Pediatric (Ped) criteria has an impact upon parents’ beliefs about their child’s illness and treatment. Methods: The data of 157 mothers and 75 fathers was used in this cross-sectional study. Parents were asked to complete a series of questionnaires including the Illness Perception Questionnaire Revised (IPQ-R) and the Treatment Representation Inventory (TRI). Parents of children, who reached the ACR Ped 70 level of improvement in arthritis were compared to parents of non-responders using Chi-Square Tests and ANOVAs. Results: A number of significant differences in parents’ illness perceptions were found. Mothers of non-responders had a stronger belief in the unpredictable nature of the arthritis (p = 0.01) and mothers of ACR Ped 70 responders showed a stronger belief in their ability to control the arthritis (p = 0.03). Fathers of ACR Pediatric 70 responders had a stronger belief in their child’s understanding of the arthritis (p = 0.01) and in the arthritis being an acute condition (p = 0.03). Only one significant difference was found in parents’ treatment representations. Mothers of ACR Ped 70 responders had a stronger belief in the ability of the treatment to cure the arthritis. The means of the scale assessing the value of treatment were high for all mothers and fathers. Other treatment and illness beliefs were in the mid-range reflecting uncertain beliefs. Conclusions: With the exception of mothers’ beliefs in the ability of the treatment to cure the arthritis, no differences were found in the treatment beliefs between parents of ACR Ped 70 responders and parents of non-responders. This suggests that with exception of beliefs in cure, the treatment success is not generally reflected in parents’ treatment beliefs. However, treatment success influenced a number of parents’ beliefs about their child’s illness. These differences were all in the expected direction. Notably, on a number of the scales mothers and fathers consistently showed a degree of uncertainty in their beliefs about their child’s illness and treatment, regardless of treatment success. This uncertainty may reflect the fact that currently there is no cure for JIA. Illness uncertainty has been found to be positively associated with negative psychological outcomes in patients with chronic illness. The findings in this study suggest that parents of children with JIA may require additional support to deal with the uncertainty in relation to their child’s illness and treatment

Geographically multifarious phenotypic divergence during speciation

Abstract Speciation is an important evolutionary process that occurs when barriers to gene flow evolve between previously panmictic populations. Although individual barriers to gene flow have been studied extensively, we know relatively little regarding the number of barriers that isolate species or whether these barriers are polymorphic within species. Herein, we use a series of field and lab experiments to quantify phenotypic divergence and identify possible barriers to gene flow between the butterfly species Lycaeides idas and Lycaeides melissa. We found evidence that L. idas and L. melissa have diverged along multiple phenotypic axes. Specifically, we identified major phenotypic differences in female oviposition preference and diapause initiation, and more moderate divergence in mate preference. Multiple phenotypic differences might operate as barriers to gene flow, as shown by correlations between genetic distance and phenotypic divergence and patterns of phenotypic variation in admixed Lycaeides populations. Although some of these traits differed primarily between species (e.g., diapause initiation), several traits also varied among conspecific populations (e.g., male mate preference and oviposition preference)

The high-precision, charge-dependent Bonn nucleon-nucleon potential (CD-Bonn)

We present a charge-dependent nucleon-nucleon (NN) potential that fits the world proton-proton data below 350 MeV available in the year of 2000 with a chi^2 per datum of 1.01 for 2932 data and the corresponding neutron-proton data with chi^2/datum = 1.02 for 3058 data. This reproduction of the NN data is more accurate than by any phase-shift analysis and any other NN potential. The charge-dependence of the present potential (that has been dubbed `CD-Bonn') is based upon the predictions by the Bonn Full Model for charge-symmetry and charge-independence breaking in all partial waves with J <= 4. The potential is represented in terms of the covariant Feynman amplitudes for one-boson exchange which are nonlocal. Therefore, the off-shell behavior of the CD-Bonn potential differs in a characteristic and well-founded way from commonly used local potentials and leads to larger binding energies in nuclear few- and many-body systems, where underbinding is a persistent problem.Comment: 69 pages (RevTex) including 20 tables and 9 figures (ps files

Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm

Background Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. This is also true for structural variation detected from sequence data. However, the genotypes at known variable sites can only be inferred with uncertainty from low coverage data. Thus, statistical approaches that infer genotype likelihoods, test hypotheses, and estimate population parameters without requiring accurate genotypes are becoming popular. Unfortunately, the current implementations of these methods are intended to analyse only single nucleotide and short indel variation, and they usually assume that the two alleles in a heterozygous individual are sampled with equal probability. This is generally false for structural variants detected with paired ends or split reads. Therefore, the population genetics of structural variants cannot be studied, unless a painstaking and potentially biased genotyping is performed first. Results We present svgem, an expectation-maximization implementation to estimate allele and genotype frequencies, calculate genotype posterior probabilities, and test for Hardy-Weinberg equilibrium and for population differences, from the numbers of times the alleles are observed in each individual. Although applicable to single nucleotide variation, it aims at bi-allelic structural variation of any type, observed by either split reads or paired ends, with arbitrarily high allele sampling bias. We test svgem with simulated and real data from the 1000 Genomes Project. Conclusions svgem makes it possible to use low-coverage sequencing data to study the population distribution of structural variants without having to know their genotypes. Furthermore, this advance allows the combined analysis of structural and nucleotide variation within the same genotype-free statistical framework, thus preventing biases introduced by genotype imputation

Genetic Analysis of Genome-Scale Recombination Rate Evolution in House Mice

The rate of meiotic recombination varies markedly between species and among individuals. Classical genetic experiments demonstrated a heritable component to population variation in recombination rate, and specific sequence variants that contribute to recombination rate differences between individuals have recently been identified. Despite these advances, the genetic basis of species divergence in recombination rate remains unexplored. Using a cytological assay that allows direct in situ imaging of recombination events in spermatocytes, we report a large (∼30%) difference in global recombination rate between males of two closely related house mouse subspecies (Mus musculus musculus and M. m. castaneus). To characterize the genetic basis of this recombination rate divergence, we generated an F2 panel of inter-subspecific hybrid males (n = 276) from an intercross between wild-derived inbred strains CAST/EiJ (M. m. castaneus) and PWD/PhJ (M. m. musculus). We uncover considerable heritable variation for recombination rate among males from this mapping population. Much of the F2 variance for recombination rate and a substantial portion of the difference in recombination rate between the parental strains is explained by eight moderate- to large-effect quantitative trait loci, including two transgressive loci on the X chromosome. In contrast to the rapid evolution observed in males, female CAST/EiJ and PWD/PhJ animals show minimal divergence in recombination rate (∼5%). The existence of loci on the X chromosome suggests a genetic mechanism to explain this male-biased evolution. Our results provide an initial map of the genetic changes underlying subspecies differences in genome-scale recombination rate and underscore the power of the house mouse system for understanding the evolution of this trait