title: Common misconceptions in molecular ecology: echoes of the modern synthesis.
abstract: The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST)  values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.
authors.affiliation: Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Kāne'ohe, HI 96744, USA. skarl@hawaii.edu
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Karl
authors.forename: R J
authors.initials: RJ
authors.lastname: Toonen
authors.forename: W S
authors.initials: WS
authors.lastname: Grant
authors.forename: B W
authors.initials: BW
authors.lastname: Bowen
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics; D019295:Computational Biology; D004272:DNA, Mitochondrial / Q000235:genetics; D004463:Ecology / Q000379:methods*; D019143:Evolution, Molecular; D005819:Genetic Markers; D005828:Genetics, Population / Q000379:methods*; D018895:Microsatellite Repeats; D008957:Models, Genetic; D008967:Molecular Biology / Q000379:methods*
chemical_list: D004272:DNA, Mitochondrial; D005819:Genetic Markers