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Joseph W Thornton

Publications and source records attributed to Joseph W Thornton.

12 recordsLinked to original sources
PubMed2025

Robustness of Ancestral Sequence Reconstruction to Among-site and Among-lineage Evolutionary Heterogeneity.

Ancestral sequence reconstruction is typically performed using homogeneous evolutionary models, which assume that the same substitution propensities affect all sites and lineages. These assumptions are routinely violated: heterogeneous structural and functional constraints favor different amino acids at different sites, and these constraints often change among lineages as epistatic substitutions accrue at other sites. To evaluate how violations of the homogeneity assumption affect ancestral sequence reconstruction under realistic conditions, we developed site-specific substitution models and parameterized them using data from deep mutational scanning experiments on three protein families; we then used these models to perform ancestral sequence reconstruction on the empirical alignments and on alignments simulated under heterogeneous conditions derived from the experiments. Extensive among-site and -lineage heterogeneity is present in these datasets, but the sequences reconstructed from empirical alignments are almost identical when heterogeneous or homogeneous models are used for ancestral sequence reconstruction. Using models fit to deep mutational scanning data from distantly related proteins in which mutational effects are very different also has a minimal impact on ancestral sequence reconstruction. The rare differences occur primarily where phylogenetic signal is weak-at fast-evolving sites and nodes connected by long branches. When ancestral sequence reconstruction is performed on simulated data, errors in the reconstructed sequences become more likely as branch lengths increase, but incorporating heterogeneity into the model does not improve accuracy. These data establish that ancestral sequence reconstruction is robust to unincorporated realistic forms of evolutionary heterogeneity, because the primary determinant of ancestral sequence reconstruction is phylogenetic signal, not the substitution model. The best way to improve accuracy is therefore not to develop more elaborate models but to apply ancestral sequence reconstruction to densely sampled alignments that maximize phylogenetic signal at the nodes of interest.

Phylogeny↗
PubMed2006

Is there a star tree paradox?

Concerns have been raised that posterior probabilities on phylogenetic trees can be unreliable when the true tree is unresolved or has very short internal branches, because existing methods for Bayesian phylogenetic analysis do not explicitly evaluate unresolved trees. Two recent papers have proposed that evaluating only resolved trees results in a "star tree paradox": when the true tree is unresolved or close to it, posterior probabilities were predicted to become increasingly unpredictable as sequence length grows, resulting in inflated confidence in one resolved tree or another and an increasing risk of false-positive inferences. Here we show that this is not the case; existing Bayesian methods do not lead to an inflation of statistical confidence, provided the evolutionary model is correct and uninformative priors are assumed. Posterior probabilities do not become increasingly unpredictable with increasing sequence length, and they exhibit conservative type I error rates, leading to a low rate of false-positive inferences. With infinite data, posterior probabilities give equal support for all resolved trees, and the rate of false inferences falls to zero. We conclude that there is no star tree paradox caused by not sampling unresolved trees.

Bayes Theorem↗
PubMed2006

The Octopus vulgaris estrogen receptor is a constitutive transcriptional activator: evolutionary and functional implications.

Steroid hormones such as estrogens and androgens are important regulators of reproduction, physiology, and development in a variety of animal taxa, including vertebrates and mollusks. Steroid hormone receptors, which mediate the classic cellular responses to these hormones, were thought to be vertebrate specific, which left the molecular mechanisms of steroid action in invertebrates unresolved. Recently an estrogen receptor (ER) ortholog was isolated from the sea hare Aplysia californica, but the functional significance of the receptor was unclear because estrogens and other steroids are not known to be important in that species. Furthermore, the Aplysia ER was found to be a constitutive transcriptional activator, but it was unclear whether the estrogen independence of the ER was an Aplysia-specific novelty or a more ancient character general to the mollusks. Here we report on the isolation and functional characterization of the first ER ortholog from an invertebrate in which estrogens are produced and play an apparent role, the cephalopod Octopus vulgaris. We show that the Octopus ER is a strong constitutive transcriptional activator from canonical estrogen response elements. The receptor does not bind estradiol and is unresponsive to estrogens and other vertebrate steroid hormones. These characteristics are similar to those observed with the Aplysia ER and support the hypothesis that the evolving ER gained constitutive activity deep in the mollusk lineage. The apparent reproductive role of estrogens in Octopus and other mollusks is unlikely to be mediated by the ER and may take place through an ancient, non-ER-mediated pathway.

Amino Acid Sequence↗
PubMed2006

Evolution of hormone-receptor complexity by molecular exploitation.

According to Darwinian theory, complexity evolves by a stepwise process of elaboration and optimization under natural selection. Biological systems composed of tightly integrated parts seem to challenge this view, because it is not obvious how any element's function can be selected for unless the partners with which it interacts are already present. Here we demonstrate how an integrated molecular system-the specific functional interaction between the steroid hormone aldosterone and its partner the mineralocorticoid receptor-evolved by a stepwise Darwinian process. Using ancestral gene resurrection, we show that, long before the hormone evolved, the receptor's affinity for aldosterone was present as a structural by-product of its partnership with chemically similar, more ancient ligands. Introducing two amino acid changes into the ancestral sequence recapitulates the evolution of present-day receptor specificity. Our results indicate that tight interactions can evolve by molecular exploitation-recruitment of an older molecule, previously constrained for a different role, into a new functional complex.

Aldosterone↗
PubMed2005

Structural analyses reveal phosphatidyl inositols as ligands for the NR5 orphan receptors SF-1 and LRH-1.

Vertebrate members of the nuclear receptor NR5A subfamily, which includes steroidogenic factor 1 (SF-1) and liver receptor homolog 1 (LRH-1), regulate crucial aspects of development, endocrine homeostasis, and metabolism. Mouse LRH-1 is believed to be a ligand-independent transcription factor with a large and empty hydrophobic pocket. Here we present structural and biochemical data for three other NR5A members-mouse and human SF-1 and human LRH-1-which reveal that these receptors bind phosphatidyl inositol second messengers and that ligand binding is required for maximal activity. Evolutionary analysis of structure-function relationships across the SF-1/LRH-1 subfamily indicates that ligand binding is the ancestral state of NR5A receptors and was uniquely diminished or altered in the rodent LRH-1 lineage. We propose that phospholipids regulate gene expression by directly binding to NR5A nuclear receptors.

Animals↗
PubMed2004

Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous.

All inferences in comparative biology depend on accurate estimates of evolutionary relationships. Recent phylogenetic analyses have turned away from maximum parsimony towards the probabilistic techniques of maximum likelihood and bayesian Markov chain Monte Carlo (BMCMC). These probabilistic techniques represent a parametric approach to statistical phylogenetics, because their criterion for evaluating a topology--the probability of the data, given the tree--is calculated with reference to an explicit evolutionary model from which the data are assumed to be identically distributed. Maximum parsimony can be considered nonparametric, because trees are evaluated on the basis of a general metric--the minimum number of character state changes required to generate the data on a given tree--without assuming a specific distribution. The shift to parametric methods was spurred, in large part, by studies showing that although both approaches perform well most of the time, maximum parsimony is strongly biased towards recovering an incorrect tree under certain combinations of branch lengths, whereas maximum likelihood is not. All these evaluations simulated sequences by a largely homogeneous evolutionary process in which data are identically distributed. There is ample evidence, however, that real-world gene sequences evolve heterogeneously and are not identically distributed. Here we show that maximum likelihood and BMCMC can become strongly biased and statistically inconsistent when the rates at which sequence sites evolve change non-identically over time. Maximum parsimony performs substantially better than current parametric methods over a wide range of conditions tested, including moderate heterogeneity and phylogenetic problems not normally considered difficult.

Bayes Theorem↗
PubMed2003

Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling.

Receptors for sex and adrenal steroid hormones are absent from fully sequenced invertebrate genomes and have not been recovered from other invertebrates. Here we report the isolation of an estrogen receptor ortholog from the mollusk Aplysia californica and the reconstruction, synthesis, and experimental characterization of functional domains of the ancestral protein from which all extant steroid receptors (SRs) evolved. Our findings indicate that SRs are extremely ancient and widespread, having diversified from a primordial gene before the origin of bilaterally symmetric animals, and that this ancient receptor had estrogen receptor-like functionality. This gene was lost in the lineage leading to arthropods and nematodes and became independent of hormone regulation in the Aplysia lineage.

Amino Acid Sequence↗
PubMed2003

Estrogen receptors in Xenopus: duplicate genes, splice variants, and tissue-specific expression.

The estrogenic steroid hormones, acting primarily through the nuclear estrogen receptors ERalpha and ERbeta, regulate sexual differentiation in a wide variety of vertebrates. In the frog Xenopus laevis, estrogen regulates the strength of vocal neuromuscular synapses and contributes to the physiological basis of sexually differentiated songs. To understand the mechanisms by which estrogen produces these effects, we have characterized the ERs of X. laevis and their expression in laryngeal muscle and other tissues. We found a remarkable molecular diversity in the estrogen receptor population within individuals. First, we have identified two distinct ERalpha genes, xlERalpha1 and xlERalpha2, which represent, to our knowledge, the first discovery of retained duplicates of the ERalpha gene in any species. These two genes are highly conserved at the amino acid level but have distinct nucleotide sequences; moreover, ERalpha2 has no N-terminal domain. Cloning of ERalpha and ERbeta in the related species Xenopus tropicalis and phylogenetic analysis indicate that the two xlERalpha loci were generated by a duplication specific to the X. laevis lineage-most likely the genome duplication that led to a doubling of the X. laevis chromosome number about 30 million years ago. The primary ER expressed in X. laevis laryngeal muscle is the novel gene xlERalpha2; ERalpha1 is primarily expressed in liver, forebrain, and oviduct. Alternatively spliced transcripts of both xlERalpha1 and xlERalpha2 are also expressed in a tissue-specific manner. We propose that complementary spatial expression of these two genes and their alternatively spliced transcripts contributes to their conservation over such a long period of time, consistent with the subfunctionalization model for evolution after gene duplication.

Amino Acid Sequence↗
PubMed2002

An automated phylogenetic key for classifying homeoboxes.

When novel gene sequences are discovered, they are usually identified, classified, and annotated based on aggregate measures of sequence similarity. This method is prone to errors, however. Phylogenetic analysis is a more accurate basis for gene classification and ortholog identification, but it is relatively labor-intensive and computationally demanding. Here we report and demonstrate a rapid new method for gene classification based on phylogenetic principles. Given the phylogeny of a minimal sample of gene family members, our method automatically identifies amino acids that are phylogenetically characteristic of each class of sequences in the family; it then classifies a novel sequence based on the presence of these characteristic attributes in its sequence. Using a subset of homeobox protein sequences as a test case, we show that our method approximates classification based on full-scale phylogenetic analysis with very high accuracy in a tiny fraction of the time.

Algorithms↗