Funds enough, and time: mtDNA, nuDNA and the discovery of divergence

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Late-Quaternary biogeographic scenarios for the brown bear (Ursus arctos), a wild mammal model species (2011, background): “Moreover, there is ongoing debate surrounding the reasons for observed discrepancies between mitochondrial and nuclear phylogeographic studies (Zink and Barrowclough, 2008; Barrowclough and Zink, 2009; Edwards and Bensch, 2009).”
Evolutionary drivers of phylogeographical diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes (2011, background): “…approach has several limitations (Funk & Omland, 2003; Ballard & Whitlock, 2004) yet it is much more likely to detect geographical limits and cryptic species than studies based on nuclear DNA gene sequences (Moore, 1995; Hudson & Coyne, 2002; Zink & Barrowclough, 2008; Barrowclough & Zink, 2009).”
Phylogeography unplugged: comparative surveys in the genomic era (2014, background): “Another major reason for keeping single locus markers in the phylogeographer’s tool kit is to advance marine phylogeography regardless of economic conditions (Barrowclough and Zink 2009).”