Estimating species trees : practical and theoretical aspects

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Multi‐gene phylogenetic analysis of south‐east Asian pest members of the Bactrocera dorsalis species complex (Diptera: Tephritidae) does not support current taxonomy (2014, methodology): “…gene trees in this study were unresolved and therefore prevented the use of the speciestree software (e.g.,Ane et al. 2007; Liu 2008; Liu et al. 2009; Kubatko 2009; Kubatko et al. 2009; Heled and Drummond 2010; Than and Nakhleh 2009; Than et al. 2008; Huang et al. 2010; Knowles and Kubatko 2010).”
Species delimitation and relationships: The dance of the seven veils (2015, methodology): “A coalescence framework should be used whenever studying closely related or sister species (Knowles & Kubatko, 2010).”
The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times (2015, methodology): “However, these methods are computationally expensive and are only practical for small datasets or when using simple nucleotide substitution models.”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, background): “For reviews of prealignment steps, see Notredame (2007), Li & Homer (2010), Kemena & Notredame (2009), Kristensen et al. (2011), Godden et al.”