Bayesian inference of recent migration rates using multilocus genotypes.
(1/35)
A new Bayesian method that uses individual multilocus genotypes to estimate rates of recent immigration (over the last several generations) among populations is presented. The method also estimates the posterior probability distributions of individual immigrant ancestries, population allele frequencies, population inbreeding coefficients, and other parameters of potential interest. The method is implemented in a computer program that relies on Markov chain Monte Carlo techniques to carry out the estimation of posterior probabilities. The program can be used with allozyme, microsatellite, RFLP, SNP, and other kinds of genotype data. We relax several assumptions of early methods for detecting recent immigrants, using genotype data; most significantly, we allow genotype frequencies to deviate from Hardy-Weinberg equilibrium proportions within populations. The program is demonstrated by applying it to two recently published microsatellite data sets for populations of the plant species Centaurea corymbosa and the gray wolf species Canis lupus. A computer simulation study suggests that the program can provide highly accurate estimates of migration rates and individual migrant ancestries, given sufficient genetic differentiation among populations and sufficient numbers of marker loci. (+info)
Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation.
(2/35)
The mutation process at microsatellite loci typically occurs at high rates and with stepwise changes in allele sizes, features that may introduce bias when using classical measures of population differentiation based on allele identity (e.g., F(ST), Nei's Ds genetic distance). Allele size-based measures of differentiation, assuming a stepwise mutation process [e.g., Slatkin's R(ST), Goldstein et al.'s (deltamu)(2)], may better reflect differentiation at microsatellite loci, but they suffer high sampling variance. The relative efficiency of allele size- vs. allele identity-based statistics depends on the relative contributions of mutations vs. drift to population differentiation. We present a simple test based on a randomization procedure of allele sizes to determine whether stepwise-like mutations contributed to genetic differentiation. This test can be applied to any microsatellite data set designed to assess population differentiation and can be interpreted as testing whether F(ST) = R(ST). Computer simulations show that the test efficiently identifies which of F(ST) or R(ST) estimates has the lowest mean square error. A significant test, implying that R(ST) performs better than F(ST), is obtained when the mutation rate, mu, for a stepwise mutation process is (a) >/= m in an island model (m being the migration rate among populations) or (b) >/= 1/t in the case of isolated populations (t being the number of generations since population divergence). The test also informs on the efficiency of other statistics used in phylogenetical reconstruction [e.g., Ds and (deltamu)(2)], a nonsignificant test meaning that allele identity-based statistics perform better than allele size-based ones. This test can also provide insights into the evolutionary history of populations, revealing, for example, phylogeographic patterns, as illustrated by applying it on three published data sets. (+info)
Altered gene expression in three plant species in response to treatment with Nep1, a fungal protein that causes necrosis.
(3/35)
Nep1 is an extracellular fungal protein that causes necrosis when applied to many dicotyledonous plants, including invasive weed species. Using transmission electron microscopy, it was determined that application of Nep1 (1.0 micro g mL(-)(1), 0.1% [v/v] Silwet-L77) to Arabidopsis and two invasive weed species, spotted knapweed (Centaurea maculosa) and dandelion (Taraxacum officinale), caused a reduction in the thickness of the cuticle and a breakdown of chloroplasts 1 to 4 h after treatment. Membrane breakdown was most severe in cells closest to the surface of application. Differential display was used to isolate cDNA clones from the three species showing differential expression in response to Nep1 treatment. Differential gene expression was observed for a putative serpin (CmSER-1) and a calmodulin-like (CmCAL-1) protein from spotted knapweed, and a putative protein phosphatase 2C (ToPP2C-1) and cytochrome P-450 (ToCYP-1) protein from dandelion. In addition, differential expression was observed for genes coding for a putative protein kinase (AtPK-1), a homolog (AtWI-12) of wound-induced WI12, a homolog (AtLEA-1) of late embryogenesis abundant LEA-5, a WRKY-18 DNA-binding protein (AtWRKY-18), and a phospholipase D (AtPLD-1) from Arabidopsis. Genes showing elevated mRNA levels in Nep1-treated (5 micro g mL(-)(1), 0.1% [v/v] Silwet-L77) leaves 15 min after Nep1 treatment included CmSER-1 and CmCAL-1 for spotted knapweed, ToCYP-1 and CmCAL-1 for dandelion, and AtPK-1, AtWRKY-18, AtWI-12, and AtLEA-1 for Arabidopsis. Levels of mRNA for AtPLD-1 (Arabidopsis) and ToPP2C-1 (dandelion) decreased rapidly in Silwet-L77-treated plants between 15 min and 4 h of treatment, but were maintained or decreased more slowly over time in Nep1-treated (5 micro g mL(-)(1), 0.1% [v/v] Silwet-L77) leaves. In general, increases in mRNA band intensities were in the range of two to five times, with only ToCYP-1 in dandelion exceeding an increase of 10 times. The identified genes have been shown to be involved or are related to gene families that are involved in plant stress responses, including wounding, drought, senescence, and disease resistance. (+info)
Allelopathy and exotic plant invasion: from molecules and genes to species interactions.
(4/35)
Here we present evidence that Centaurea maculosa (spotted knapweed), an invasive species in the western United States, displaces native plant species by exuding the phytotoxin (-)-catechin from its roots. Our results show inhibition of native species' growth and germination in field soils at natural concentrations of (-)-catechin. In susceptible species such as Arabidopsis thaliana, the allelochemical triggers a wave of reactive oxygen species (ROS) initiated at the root meristem, which leads to a Ca2+ signaling cascade triggering genome-wide changes in gene expression and, ultimately, death of the root system. Our results support a "novel weapons hypothesis" for invasive success. (+info)
Inheritance of resistance to clopyralid and picloram in yellow starthistle (Centaurea solstitialis L.) is controlled by a single nuclear recessive gene.
(5/35)
The noxious weed yellow starthistle (Centaurea solstitialis L.) can be controlled effectively at the seedling stage with foliar application of the auxinic herbicides picloram or clopyralid. Although resistance to these herbicides is rare, a yellow starthistle biotype resistant to picloram and cross-resistant to clopyralid was observed in 1989 near Dayton, WA, in a pasture that had been subjected to intensive picloram selective pressure. Our objective was to determine the mode of inheritance for this resistance trait. Transmission of the resistant phenotype was monitored in reciprocal F(1) crosses between susceptible (SCI) and resistant (RDW) plants, their testcross and pseudo-F(2) progeny. Progeny from all crosses, as well as RDW and SCI seedlings of original populations, were sprayed with picloram or clopyralid to distinguish between susceptible and resistant individuals. All F(1) progeny were susceptible to both herbicides, indicating that the resistance trait was of nuclear origin and recessive in nature. Segregation of the resistant phenotype among pseudo-F(2) and testcross progeny of F(1) genotypes demonstrated monofactorial inheritance (P >.25) for resistance to both herbicides. The conclusion that resistance is conferred by a single recessive allele is consistent with the observation that no other picloram-resistant yellow starthistle populations have been identified in the area since picloram selection pressure was abated. (+info)
Realistic species losses disproportionately reduce grassland resistance to biological invaders.
(6/35)
Consequences of progressive biodiversity declines depend on the functional roles of individual species and the order in which species are lost. Most studies of the biodiversity-ecosystem functioning relation tackle only the first of these factors. We used observed variation in grassland diversity to design an experimental test of how realistic species losses affect invasion resistance. Because entire plant functional groups disappeared faster than expected by chance, resistance declined dramatically with progressive species losses. Realistic biodiversity losses, even of rare species, can thus affect ecosystem processes far more than indicated by randomized-loss experiments. (+info)
Fine-scale genetic structure and gene dispersal in Centaurea corymbosa (Asteraceae). II. Correlated paternity within and among sibships.
(7/35)
The fine-scale pattern of correlated paternity was characterized within a population of the narrow-endemic model plant species, Centaurea corymbosa, using microsatellites and natural progeny arrays. We used classical approaches to assess correlated mating within sibships and developed a new method based on pairwise kinship coefficients to assess correlated paternity within and among sibships in a spatio-temporal perspective. We also performed numerical simulations to assess the relative significance of different mechanisms promoting correlated paternity and to compare the statistical properties of different estimators of correlated paternity. Our new approach proved very informative to assess which factors contributed most to correlated paternity and presented good statistical properties. Within progeny arrays, we found that about one-fifth of offspring pairs were full-sibs. This level of correlated mating did not result from correlated pollen dispersal events (i.e., pollen codispersion) but rather from limited mate availability, the latter being due to limited pollen dispersal distances, the heterogeneity of pollen production among plants, phenological heterogeneity and, according to simulations, the self-incompatibility system. We point out the close connection between correlated paternity and the "TwoGener" approach recently developed to infer pollen dispersal and discuss the conditions to be met when applying the latter. (+info)
Centaurea revisited: A molecular survey of the Jacea group.
(8/35)
BACKGROUND AND AIMS: The genus Centaurea has traditionally been considered to be a complicated taxon. No attempt at phylogenetic reconstruction has been made since recent revisions in circumscription, and previous reconstructions did not include a good representation of species. A new molecular survey is thus needed. METHODS: Phylogenetic analyses were conducted using sequences of the internal transcribed spacers (ITS) 1 and 2 and the 5.8S gene. Parsimony and Bayesian approaches were used. KEY RESULTS: A close correlation between geography and the phylogenetic tree based on ITS sequences was found in all the analyses, with three main groups being resolved: (1) comprising the most widely distributed circum-Mediterranean/Eurosiberian sections; (2) the western Mediterranean sections; and (3) the eastern Mediterranean and Irano-Turanian sections. The results show that the sectional classification in current use needs major revision, with many old sections being merged into larger ones. A large polytomy in the eastern Mediterranean clade suggests a rapid and recent speciation in this group. Some inconsistencies between morphology and molecular phylogeny may indicate that hybridization has played a major role in the evolution of the genus. CONCLUSIONS: Phylogenetic analysis of ITS has been useful in identifying the major lineages in the group, and unraveling many inconsistencies in the sectional classification. However, most recent groups in the eastern Mediterranean clade are not resolved and reticulation in the western Mediterranean group of sections makes phylogenetic relationships within these two groups somewhat obscure. (+info)