@article{aris-brosou_2005, title={Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis}, volume={22}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msi006}, abstractNote={To explain why informational genes (i.e., those involved in transcription, translation, and related processes) are less likely than housekeeping genes to be horizontally transferred, Jain and coworkers proposed the complexity hypothesis. The underlying idea is that informational genes belong to large, complex systems of coevolving genes. Consequently, the likelihood of the successful horizontal transfer of a single gene from such an integrated system is expected to be low. Here, this hypothesis is extended to explain some of the determinants of the mode of evolution of coding sequences. It is proposed that genes belonging to complex systems are relatively less likely to be under adaptive evolution. To evaluate this "extended complexity hypothesis," 2,428 families and protein domains were analyzed. This analysis found that genes whose products are highly connected, located in intracellular components, and involved in complex processes and functions were more conserved and less likely to be under adaptive evolution than are other gene products. The extended complexity hypothesis suggests that both the mode and the rate of evolution of a protein are influenced by its gene ontology (localization, biological process, and molecular function) and by its connectivity.}, number={2}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Aris-Brosou, S}, year={2005}, month={Feb}, pages={200–209} }
 @article{aris-brosou_yang_2003, title={Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa}, volume={20}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msg226}, abstractNote={Multicellular animals, or Metazoa, appear in the fossil records between 575 and 509 million years ago (MYA). At odds with paleontological evidence, molecular estimates of basal metazoan divergences have been consistently older than 700 MYA. However, those date estimates were based on the molecular clock hypothesis, which is almost always violated. To relax this hypothesis, we have implemented a Bayesian approach to describe the change of evolutionary rate over time. Analysis of 22 genes from the nuclear and the mitochondrial genomes under the molecular clock assumption produced old date estimates, similar to those from previous studies. However, by allowing rates to vary in time and by taking small species-sampling fractions into account, we obtained much younger estimates, broadly consistent with the fossil records. In particular, the date of protostome-deuterostome divergence was on average 582 +/- 112 MYA. These results were found to be robust to specification of the model of rate change. The clock assumption thus had a dramatic effect on date estimation. However, our results appeared sensitive to the prior model of cladogenesis, although the oldest estimates (791 +/- 246 MYA) were obtained under a suboptimal model. Bayes posterior estimates of evolutionary rates indicated at least one major burst of molecular evolution at the end of the Precambrian when protostomes and deuterostomes diverged. We stress the importance of assumptions about rates on date estimation and suggest that the large discrepancies between the molecular and fossil dates of metazoan divergences might partly be due to biases in molecular date estimation.}, number={12}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Aris-Brosou, S and Yang, ZH}, year={2003}, month={Dec}, pages={1947–1954} }
 @article{aris-brosou_2003, title={How Bayes tests of molecular phylogenies compare with frequentist approaches}, volume={19}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/btg065}, abstractNote={Abstract}, number={5}, journal={BIOINFORMATICS}, author={Aris-Brosou, S}, year={2003}, month={Mar}, pages={618–624} }
 @article{aris-brosou_2003, title={Least and most powerful phylogenetic tests to elucidate the origin of the seed plants in the presence of conflicting signals under misspecified models}, volume={52}, ISSN={["1076-836X"]}, DOI={10.1080/10635150390258949}, abstractNote={Several tests of molecular phylogenies have been proposed over the last decades, but most of them lead to strikingly different P-values. I propose that such discrepancies are principally due to different forms of null hypotheses. To support this hypothesis, two new tests are described. Both consider the composite null hypothesis that all the topologies are equidistant from the true but unknown topology. This composite hypothesis can either be reduced to the simple hypothesis at the least favorable distribution (frequentist significance test (FST)) or to the maximum likelihood topology (frequentist hypothesis test (FHT)). In both cases, the reduced null hypothesis is tested against each topology included in the analysis. The tests proposed have an information-theoretic justification, and the distribution of their test statistic is estimated by a nonparametric bootstrap, adjusting P-values for multiple comparisons. I applied the new tests to the reanalysis of two chloroplast genes, psaA and psbB, and compared the results with those of previously described tests. As expected, the FST and the FHT behaved approximately like the Shimodaira-Hasegawa test and the bootstrap, respectively. Although the tests give overconfidence in a wrong tree when an overly simple nucleotide substitution model is assumed, more complex models incorporating heterogeneity among codon positions resolve some conflicts. To further investigate the influence of the null hypothesis, a power study was conducted. Simulations showed that FST and the Shimodaira-Hasegawa test are the least powerful and FHT is the most powerful across the parameter space. Although the size of all the tests is affected by misspecification, the two new tests appear more robust against misspecification of the model of evolution and consistently supported the hypothesis that the Gnetales are nested within gymnosperms. (Approximately unbiased test; bootstrap proportion; hypothesis test; P-value adjustment; Shimodaira-Hasegawa test; significance test.)}, number={6}, journal={SYSTEMATIC BIOLOGY}, author={Aris-Brosou, S}, year={2003}, month={Dec}, pages={781–793} }