A Bayesian Model for Gene Family Evolution

Background A birth and death process is frequently used for modeling the size of a gene family that may vary along the branches of a phylogenetic tree. Under the birth and death model, maximum likelihood methods have been developed to estimate the birth and death rate and the sizes of ancient gene families (numbers of gene copies at the internodes of the phylogenetic tree). This paper aims to provide a Bayesian approach for estimating parameters in the birth and death model. Results We develop a Bayesian approach for estimating the birth and death rate and other parameters in the birth and death model. In addition, a Bayesian hypothesis test is developed to identify the gene families that are unlikely under the birth and death process. Simulation results suggest that the Bayesian estimate is more accurate than the maximum likelihood estimate of the birth and death rate. The Bayesian approach was applied to a real dataset of 3517 gene families across genomes of five yeast species. The results indicate that the Bayesian model assuming a constant birth and death rate among branches of the phylogenetic tree cannot adequately explain the observed pattern of the sizes of gene families across species. The yeast dataset was thus analyzed with a Bayesian heterogeneous rate model that allows the birth and death rate to vary among the branches of the tree. The unlikely gene families identified by the Bayesian heterogeneous rate model are different from those given by the maximum likelihood method. Conclusions Compared to the maximum likelihood method, the Bayesian approach can produce more accurate estimates of the parameters in the birth and death model. In addition, the Bayesian hypothesis test is able to identify unlikely gene families based on Bayesian posterior p-values. As a powerful statistical technique, the Bayesian approach can effectively extract information from gene family data and thereby provide useful information regarding the evolutionary process of gene families across genomes

A Bayesian model for gene family evolution

Abstract Background A birth and death process is frequently used for modeling the size of a gene family that may vary along the branches of a phylogenetic tree. Under the birth and death model, maximum likelihood methods have been developed to estimate the birth and death rate and the sizes of ancient gene families (numbers of gene copies at the internodes of the phylogenetic tree). This paper aims to provide a Bayesian approach for estimating parameters in the birth and death model. Results We develop a Bayesian approach for estimating the birth and death rate and other parameters in the birth and death model. In addition, a Bayesian hypothesis test is developed to identify the gene families that are unlikely under the birth and death process. Simulation results suggest that the Bayesian estimate is more accurate than the maximum likelihood estimate of the birth and death rate. The Bayesian approach was applied to a real dataset of 3517 gene families across genomes of five yeast species. The results indicate that the Bayesian model assuming a constant birth and death rate among branches of the phylogenetic tree cannot adequately explain the observed pattern of the sizes of gene families across species. The yeast dataset was thus analyzed with a Bayesian heterogeneous rate model that allows the birth and death rate to vary among the branches of the tree. The unlikely gene families identified by the Bayesian heterogeneous rate model are different from those given by the maximum likelihood method. Conclusions Compared to the maximum likelihood method, the Bayesian approach can produce more accurate estimates of the parameters in the birth and death model. In addition, the Bayesian hypothesis test is able to identify unlikely gene families based on Bayesian posterior p-values. As a powerful statistical technique, the Bayesian approach can effectively extract information from gene family data and thereby provide useful information regarding the evolutionary process of gene families across genomes.</p

Multi-Generational Kinship, Multiple Mating, and Flexible Modes of Parental Care in a Breeding Population of the Veery (Catharus fuscescens), a Trans-Hemispheric Migratory Songbird.

We discovered variable modes of parental care in a breeding population of color-banded Veeries (Catharus fuscescens), a Nearctic-Neotropical migratory songbird, long thought to be socially monogamous, and performed a multi-locus DNA microsatellite analysis to estimate parentage and kinship in a sample of 37 adults and 21 offspring. We detected multiple mating in both sexes, and four modes of parental care that varied in frequency within and between years including multiple male feeders at some nests, and males attending multiple nests in the same season, each with a different female. Unlike other polygynandrous systems, genetic evidence indicates that multi-generational patterns of kinship occur among adult Veeries at our study site, and this was corroborated by the capture of an adult male in 2013 that had been banded as a nestling in 2011 at a nest attended by multiple male feeders. All genotyped adults (n = 37) were related to at least one other bird in the sample at the cousin level or greater (r ≥ 0.125), and 81% were related to at least one other bird at the half-sibling level or greater (r ≥ 0.25, range 0.25-0.60). Although our sample size is small, it appears that the kin structure is maintained by natal philopatry in both sexes, and that Veeries avoid mating with close genetic kin. At nests where all adult feeders were genotyped (n = 9), the male(s) were unrelated to the female (mean r = -0.11 ± 0.15), whereas genetic data suggest close kinship (r = 0.254) between two male co-feeders at the nests of two females in 2011, and among three of four females that were mated to the same polygynous male in 2012. To our knowledge, this is the first evidence of polygynandry occurring among multiple generations of close genetic kin on the breeding ground of a Nearctic-Neotropical migratory songbird

HIGHER CONCENTRATION OF Fe LEADS TO HISTONE MODIFICATION IN COMMON BEAN TISSUE

INTRODUCTION Over more than 100 years agricultural scientists all over the world have developed high yielding crop varieties to meet the energy demand of increasing population. However the nutritional qualities have not been given priorities as a result world is facing with serious malnutrition problem. Two of the most prominent deficiencies affecting the world are of iron (Fe) and zinc (Zn). Among others Fe is vital in building proteins of red blood cells, whereas Zn is essential in cellular growth and development. Epigenetic mechanisms such as DNA methylation, histone modification, and small interfering RNA (sRNA) regulate the transcription of DNA in living organisms (He et al. 2011). It has been reported that the abiotic and biotic stresses such as changes in temperature, pests, drought, disease, and the concentration of minerals and metals in the surrounding soil are involved with the changes in epigenetic and transcriptomic components (Hu et al. 2012) in plant. The long-terms goals of our work are to identify the epigenetic and transcriptomic components involved in the acquisition and translocation of micronutrients in common bean. MATERIALS AND METHODS In our work, we applied higher concentrations of Fe to a common bean genotype G122 which was previously identified as a genotype that is highly responsive to elevated Fe and other health-related minerals (Bauduin et al. 2014). The treated and control plants were planted in 8.5”x11” pots filled with Sunshine Mix. The sunshine mix was kept soaked with water until germination. After germination we kept the clear saucers beneath the treated pot filled with a solution of Fe (200 mg-1L) until the leaves reached 50% senescence while the control plant continued to receive water. At 50% leaf senescence, the stems of the plants were harvested and chromatin and total histone were isolated using the Chromaflash Plant Chromatin Extraction Kit (P-2022) and Epiquik Total Extraction Kit (OP-0006) respectively (www.epigenetek.com). One hundred nanograms of total histone of treated and control samples were added into the wells of 20 H3 modification sites in duplication for identifying each of the 20 histone modification patterns. Following the procedure described in the EpiQuik Histone H3 Modification Multiplex Assay Kit (P-3100), the intensity of absorbance of the H3 modification sites was measured at 450 nm wavelength by a BioTek Microplate reader (Elx808). Using the formula (given below) provided by the EpiQuik Histone H3 Modification Multiplex Assay Kit, histone modifications for 20 of the 21 H3 modification sites were calculated in ng/μg of histone 3 protein and compared between treated and control stems and presented as fold change (Table. 1)

Allele frequency and polymorphism data for six microsatellite markers amplified from 37 adult Veeries (<i>Catharus fuscescens</i>) and 21 offspring at White Clay Creek State Park, New Castle County, Delaware.

<p>Data were calculated via CERVUS 3.0.</p

Patterns of feeding and parentage at nests of the Veery (<i>n</i> = 14) during the 2011 and 2012 breeding seasons at White Clay Creek State Park, New Castle County, Delaware.

<p>Males and females are denoted by gray and white circles, respectively. One female in 2011 was unbanded (UNK). Solid lines represent feeding relationships between adults and the nests they attended (black circles). Double solid lines denote feeding and parentage. Dashed lines represent parentage only (i.e., extra-pair fertilizations), as determined via parental exclusion. LXMA fathered one nestling in the nest attended by his close relative AXRO (<i>r</i> = 0.254) and female XWRY. An unknown father (?) sired one nestling in the nest attended by AXRO and female LGOX. The 2012 brood fed by XARR and MBXY was not genotyped. One nest in 2011 was attended by a heterospecific adult, denoted "WOTH" [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157051#pone.0157051.ref045" target="_blank">45</a>].</p

Summary of genetic relatedness in a sample of 37 adult Veeries (<i>n</i> = 666 pairwise combinations) from White Clay Creek State Park, New Castle County, Delaware.

<p>Data represent <i>r</i>-values for genotype pairs derived from six polymorphic microsatellite loci [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157051#pone.0157051.ref033" target="_blank">33</a>], as calculated via KINGROUP 2.0.</p

(2011) Still image from digital video showing female GRXL during a food delivery to nestlings B/OX and B/WX on June 11, 2011.

<p>This nest was also provisioned by two closely related males (AXRO and LXMA, <i>r</i> = 0.254). (2012) Still image from video showing GRXL in agonistic posture (i.e., "horizontal stretch" with bill gaping) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157051#pone.0157051.ref044" target="_blank">44</a>] immediately prior to the arrival of AXRO (see text for context). (2014) Digital photograph of B/OX as an adult male, 22 May 2014 (photo by M. Gutierrez-Ramirez). As an adult, B/OX was first detected at the site in 2013. All images were taken at White Clay Creek State Park, New Castle County, Delaware.</p

Radiation Hybrid Mapping of the Species Cytoplasm-Specific (scs(ae)) Gene in Wheat

Radiation hybrid (RH) mapping is based on radiation-induced chromosome breakage and analysis of chromosome segment retention or loss using molecular markers. In durum wheat (Triticum turgidum L., AABB), an alloplasmic durum line [(lo) durum] has been identified with chromosome 1D of T. aestivum L. (AABBDD) carrying the species cytoplasm-specific (scs(ae)) gene. The chromosome 1D of this line segregates as a whole without recombination, precluding the use of conventional genome mapping. A radiation hybrid mapping population was developed from a hemizygous (lo) scs(ae)− line using 35 krad gamma rays. The analysis of 87 individuals of this population with 39 molecular markers mapped on chromosome 1D revealed 88 radiation-induced breaks in this chromosome. This number of chromosome 1D breaks is eight times higher than the number of previously identified breaks and should result in a 10-fold increase in mapping resolution compared to what was previously possible. The analysis of molecular marker retention in our radiation hybrid mapping panel allowed the localization of scs(ae) and 8 linked markers on the long arm of chromosome 1D. This constitutes the first report of using RH mapping to localize a gene in wheat and illustrates that this approach is feasible in a species with a large complex genome