scholarly journals Repeated evolution of a morphological novelty: a phylogenetic analysis of the inflated fruiting calyx in the Physalideae tribe (Solanaceae)

2018 ◽  
Author(s):  
Rocío Deanna ◽  
Maximilien D. Larter ◽  
Gloria E. Barboza ◽  
Stacey D. Smith
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Phylogenetic Signal ◽  
Model Fitting ◽  
Trait Evolution ◽  
Parsimony Score ◽  
Likelihood Model ◽  
Best Fitting ◽  
Stochastic Mapping ◽  
Gains And Losses

PREMISE OF THE STUDYThe evolution of novel fruit morphologies has been integral to the success of angiosperms. The inflated fruiting calyx, in which the balloon-like calyx swells to completely surround the fruit, has evolved repeatedly across angiosperms and is postulated to aid in protection and dispersal. Here we investigate the evolution of this trait in the tomatillos and their allies (Physalideae, Solanaceae), using a newly estimated phylogeny and a suite of comparative methods to infer evolutionary gains and losses.METHODSThe Physalideae phylogeny was estimated using DNA sequences from four regions (ITS, LEAFY, trnL-F, waxy) using maximum likelihood and Bayesian Inference. Maximum likelihood model selection was used to determine the best fitting model of trait evolution. Using this model, we estimated ancestral states along with the numbers of gains and losses of fruiting calyx accrescence and inflation with Bayesian stochastic mapping. Also, phylogenetic signal in calyx morphology was examined with two metrics (parsimony score and Fritz and Purvis’ D).KEY RESULTSThe well resolved phylogeny points to multiple taxa in need of revision, including the eight genera that are non-monophyletic as presently circumscribed. Model fitting indicated that calyx evolution has proceeded in stepwise fashion, from non-accrescent, to accrescent, to inflated. Moreover, these transitions appear to be largely irreversible. Among the 215 sampled Physalideae, we inferred 24 gains of fruiting calyx accrescence, 24 subsequent transitions to a fully inflated calyx and only two reversals. A median of 50 shifts were estimated in total across the clade from the ancestral non-accrescent calyx. Nonetheless, fruiting calyx accrescence and inflation show strong phylogenetic signal.CONCLUSIONSOur phylogeny greatly improves the resolution of Physalideae and highlights the need for taxonomic work. The analyses of trait evolution reveal that the inflated fruiting calyx has evolved many times and that the trajectory towards this phenotype is generally stepwise and directional. These results provide a strong foundation for studying the genetic and developmental mechanisms responsible for the repeated origins of this charismatic fruit trait.

scholarly journals Maximum-likelihood model fitting for quantitative analysis of SMLM data

2021 ◽  
Author(s):  
Yu-Le Wu ◽  
Philipp Hoess ◽  
Aline Tschanz ◽  
Ulf Matti ◽  
Markus Mund ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Maximum Likelihood ◽  
Single Molecule ◽  
Model Fitting ◽  
Super Resolution ◽  
Likelihood Estimation ◽  
Nuclear Pore ◽  
Analysis Workflow ◽  
Likelihood Model ◽  
Protein Density

Quantitative analysis is an important part of any single-molecule localization microscopy (SMLM) data analysis workflow to extract biological insights from the coordinates of the single fluorophores, but current approaches are restricted to simple geometries or do not work on heterogenous structures. Here, we present LocMoFit (Localization Model Fit), an open-source framework to fit an arbitrary model directly to the localization coordinates in SMLM data. Using maximum likelihood estimation, this tool extracts the most likely parameters for a given model that best describe the data, and can select the most likely model from alternative models. We demonstrate the versatility of LocMoFit by measuring precise dimensions of the nuclear pore complex and microtubules. We also use LocMoFit to assemble static and dynamic multi-color protein density maps from thousands of snapshots. In case an underlying geometry cannot be postulated, LocMoFit can perform single-particle averaging of super-resolution structures without any assumption about geometry or symmetry. We provide extensive simulation and visualization routines to validate the robustness of LocMoFit and tutorials based on example data to enable any user to increase the information content they can extract from their SMLM data.

Altruism and Genetics

1984 ◽  
Vol 33 (2) ◽  
pp. 265-271 ◽  
Author(s):  
J.P. Rushton ◽  
D.W. Fulker ◽  
M.C. Neale ◽  
R.A. Blizard ◽  
H.J. Eysenck
Keyword(s):  
Maximum Likelihood ◽  
Construct Validity ◽  
Model Fitting ◽  
Genetic Effects ◽  
Self Report ◽  
Same Sex ◽  
Common Environment ◽  
Likelihood Model ◽  
Empathy Scale ◽  
The University

AbstractThree questionnaires measuring altruistic tendencies were completed by 573 adult twin pairs from the University of London Institute of Psychiatry Volunteer Twin Register. The questionnaires consisted of a 20-item Self-Report Altruism Scale, a 33-item Empathy Scale, and a 16-item Nurturance Scale, all of which had previously been shown to have construct validity. For the three scales, the intra-class correlations for the 296 MZ pairs were 0.53, 0.54, and 0.49, and for the 179 same-sex DZ pairs were 0.25,020, and 0.14, giving rough estimates of broad heritability of 56%, 68%, and 72%, respectively. Maximum-likelihood model-fitting revealed about 50% of the variance on each scale to be associated with genetic effects, virtually 0% to be due to the twins' common environment, and the remaining 50% to be due to each twins' specific environment and/or error associated with the test.

scholarly journals Development of a joint evolutionary model for the genome and the epigenome

2018 ◽  
Author(s):  
Jia Lu ◽  
Xiaoyi Cao ◽  
Sheng Zhong
Keyword(s):  
Dna Sequences ◽  
Model Fitting ◽  
Joint Probability ◽  
Evolutionary Model ◽  
Simplex Algorithm ◽  
Likelihood Method ◽  
Genome Comparison ◽  
Sequence Dependent ◽  
Downhill Simplex ◽  
Gains And Losses

AbstractBackgroundInterspecies epigenome comparisons yielded functional information that cannot be revealed by genome comparison alone, begging for theoretical advances that enable principled analysis approaches. Whereas probabilistic genome evolution models provided theoretical foundation to comparative genomics studies, it remains challenging to extend DNA evolution models to epigenomes.ResultsWe present an effort to develop ab initio evolution models for epigenomes, by explicitly expressing the joint probability of multispecies DNA sequences and histone modifications on homologous genomic regions. This joint probability is modeled as a mixture of four components representing four evolutionary hypotheses, namely dependence and independence of interspecies epigenomic variations to sequence mutations and to sequence insertions and deletions (indels). For model fitting, we implemented a maximum likelihood method by coupling downhill simplex algorithm with dynamic programming. Based on likelihood comparisons, the model can be used to infer whether interspecies epigenomic variations depend on mutation or indels in local genomic sequences. We applied this model to analyze DNase hypersensitive regions and spermatid H3K4me3 ChIP-seq data from human and rhesus macaque. Approximately 5.5% of homologous regions in the genomes exhibited H3K4me3 modification in either species, among which approximately 67% homologous regions exhibited sequence-dependent interspecies H3K4me3 variations. Mutations accounted for less sequence-dependent H3K4me3 variations than indels. Among transposon-mediated indels, ERV1 insertions and L1 insertions were most strongly associated with H3K4me3 gains and losses, respectively.ConclusionThis work initiates a class of probabilistic evolution models that jointly model the genomes and the epigenomes, thus helps to bring evolutionary principles to comparative epigenomic studies.

scholarly journals A Chromosome-Based Model for Estimating the Number of Conserved Segments Between Pairs of Species From Comparative Genetic Maps

Genetics ◽  
2000 ◽  
Vol 154 (1) ◽  
pp. 323-332
Author(s):  
David Waddington ◽  
Anthea J Springbett ◽  
David W Burt
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Common Ancestor ◽  
Length Distribution ◽  
Genetic Maps ◽  
Segment Length ◽  
Syntenic Block ◽  
Comparative Maps

Abstract Comparative genetic maps of two species allow insights into the rearrangements of their genomes since divergence from a common ancestor. When the map details the positions of genes (or any set of orthologous DNA sequences) on chromosomes, syntenic blocks of one or more genes may be identified and used, with appropriate models, to estimate the number of chromosomal segments with conserved content conserved between species. We propose a model for the distribution of the lengths of unobserved segments on each chromosome that allows for widely differing chromosome lengths. The model uses as data either the counts of genes in a syntenic block or the distance between extreme members of a block, or both. The parameters of the proposed segment length distribution, estimated by maximum likelihood, give predictions of the number of conserved segments per chromosome. The model is applied to data from two comparative maps for the chicken, one with human and one with mouse.

Systematic status of Campydora Cobb, 1920 (Nematoda: Campydorina)

Nematology ◽  
2003 ◽  
Vol 5 (5) ◽  
pp. 699-711 ◽  
Author(s):  
Peter Mullin ◽  
Timothy Harris ◽  
Thomas Powers
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Systematic Position ◽  
Nominal Species ◽  
Competing Hypotheses ◽  
Small Subunit Ribosomal Dna

AbstractThe systematic position of Campydora Cobb, 1920, which possesses many unique morphological features, especially in pharyngeal structure and stomatal armature, has long been a matter of uncertainty with the 'position of the Campydorinae' (containing only Campydora) being questionable. A review of the morphology of C. demonstrans, the only nominal species of Campydora concluded that the species warranted placement as the sole member of a monotypic suborder, Campydorina, in the order Dorylaimida. Others placed Campydorina in the order Enoplida. We conducted phylogenetic analyses, using 18s small subunit ribosomal DNA sequences generated from a number of taxa in the subclasses Enoplia and Dorylaimia, to evaluate these competing hypotheses. Although precise taxonomic placement of the genus Campydora and the identity of its closest living relatives is in need of further investigation, our analyses, under maximum parsimony, distance, and maximum likelihood criteria, unambiguously indicate that Campydora shares a common, more recent, ancestry with genera such as Alaimus, Pontonema, Tripyla and Ironus (Enoplida), rather than with any members of Dorylaimida, Mononchida or Triplonchida.

Towards a monophyletic classification of Lejeuneaceae III: the systematic position of Leiolejeunea

Phytotaxa ◽  
2014 ◽  
Vol 170 (3) ◽  
pp. 187 ◽  
Author(s):  
ALFONS SCHÄFER-VERWIMP ◽  
KATHRIN FELDBERG ◽  
SHANSHAN DONG ◽  
HUUB VAN MELICK ◽  
DENILSON F. PERALTA ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Its Region ◽  
Systematic Position ◽  
Leaf Cell ◽  
Oil Bodies ◽  
Sister Relationship ◽  
First Time

The derived liverwort Leiolejeunea grandiflora was recollected at the type locality in Jamaica after more than 100 years. The characteristics of its oil bodies were described for the first time based on the new collections. Each leaf cell possesses 2-4(-6) rather small, subhomogeneous to very finely segmented, subglobose to ellipsoidal, colorless oil bodies. The plants were either dioicous or autoicous. DNA sequences of two chloroplast regions (trnL-trnF, rbcL) and the nuclear ribosomal ITS region were obtained for two accessions of Leiolejeunea to enable the inference of the phylogenetic relationships of these plants. Based on Bayesian inference of phylogeny as well as maximum parsimony and maximum likelihood analyses of a dataset including 87 representatives of Lejeuneaceae, Leiolejeunea was found as the putative sister to either Echinolejeuneinae or Cheilolejeuneinae. Thus, we propose the new monogeneric subtribe Leiolejeuneinae with relationships to Cheilolejeuneinae and Echinolejeuneinae. The analyses included also one accession of the generitype of Cheilolejeunea, C. decidua [= Cheilolejeunea adnata]. This species was found in a well supported sister relationship with Cystolejeunea. To avoid nomenclatural confusion, we propose a wide genus concept for Cheilolejeunea including Aureolejeunea, Cyrtolejeunea, Cystolejeunea, Evansiolejeunea, Leucolejeunea, and Omphalanthus.

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