Molecular phylogenetics: principles and practice

By Ziheng Yang, Bruce Rannala. 2012

728 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. R. Beutel
2. Michael Whiting
3. R. Leschen
4. J. McHugh
5. Xing‐Xing Shen
6. Kangshan Mao
7. Xiaofan Zhou
8. A. Eckert

In Molecular Biology

1. Michael Whiting
2. Xing‐Xing Shen
3. J. McHugh
4. Xiaofan Zhou
5. A. Eckert
6. A. Ślipiński
7. Jianquan Liu
8. A. Yassin

In Paleontology

1. Michael Whiting
2. A. Ślipiński
3. D. Mckenna
4. Xiaofan Zhou
5. Jianquan Liu
6. Xing‐Xing Shen
7. A. Yassin
8. Laura Boykin

Citations in the corpus

• How to build phylogenetic species trees with OMA (2020, neutral): “For more information about the theory behind phylogenomics and the different methods, we refer the reader to recent reviews 25–27 .”
• Phylogenetic classification of the Drosophilidae Rondani (Diptera): the role of morphology in the postgenomic era (2013, methodology): “Given the large proportion of missing data, only Bayesian methods were used to infer the phylogenetic hypotheses from the concatenated matrix without partition because this is known to be the most robust against missing data (Yang & Rannala, 2012).”
• Evolutionary origin of species diversity on the Qinghai–Tibet Plateau (2021, background): “…clock models, better strategies to integrate fossils and upgraded techniques to extract fossil information, have improved the molecular dating approaches for timing divergence events (e.g., Yang & Rannala, 2012; Wen et al., 2013; Heath et al., 2014; Ho & Duchene, 2014; dos Reis et al., 2016).”
• A practical guide to identifying members of the Bemisia tabaci species complex: and other morphologically identical species (2014, background): “There are many different options for phylogenetic analyses (Yang and Rannala, 2012) and species delimitation (Rannala and Yang, 2013) beyond the B. tabaci literature.”
• The beetle tree of life reveals that Coleoptera survived end‐Permian mass extinction to diversify during the Cretaceous terrestrial revolution (2015, result): “40, 835–880 Some differences between our results and the results of previous studies, particularly at higher taxonomic levels, are clearly due to differences in rooting and outgroups (or lack thereof) (e.g. Caterino et al., 2002; Yang & Rannala, 2012).”
• Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets (2017, background): “It is now generally accepted that statistical methods, such as maximum likelihood (ML) (Felsenstein 1981), produce more reliable results than distance and parsimony methods (Yang and Rannala 2012; Whelan and Morrison 2017).”
• The emerging field of geogenomics: Constraining geological problems with genetic data (2014, methodology): “For example, statistical methods are available for use of single or multiple calibration points in molecular phylogenies that incorporate fossils that are distantly related to the focal taxon (Wertheim et al., 2010; Yang and Rannala, 2012).”