INVITED REVIEW
You have free access to this content
Common misconceptions in molecular ecology: echoes of the modern synthesis

Article first published online: 11 MAY 2012
DOI: 10.1111/j.1365-294X.2012.05576.x
© 2012 Blackwell Publishing Ltd
Additional Information
How to Cite
KARL, S. A., TOONEN, R. J., GRANT, W. S. and BOWEN, B. W. (2012), Common misconceptions in molecular ecology: echoes of the modern synthesis. Molecular Ecology, 21: 4171–4189. doi: 10.1111/j.1365-294X.2012.05576.x
Publication History
- Issue published online: 23 AUG 2012
- Article first published online: 11 MAY 2012
- Received 16 December 2011; revision received 21 February 2012; accepted 7 March 2012
References
- (1994) Molecular Markers, Natural History, and Evolution. Chapman & Hal, Inc. New York, NY.
- (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, MA.
- , , et al. (1998) Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific. Molecular Ecology, 7, 695–707.
- , (2004) The incomplete history of mitochondria. Molecular Ecology, 13, 729–744.
- (1763) An essay towards solving a problem in the doctrine of chances. Philosophical Transactions of the Royal Society of London 53, 370–418.
- , , (2006) Population size does not influence mitochondrial genetic diversity in animals. Science, 312, 570–572.
- (2003) The manuscript review process: the proper roles of authors, referees, and editor. Journal of Management Inquiry, 12, 331–338.
- , , (1997) Fish biogeography and molecular clocks: perspectives from the Panama Isthmus. In: Molecular Systematic of Fishes (eds Kocher TD, Stepien CA), pp. 113–126, Academic Press, San Diego, CA.
- , , , (2011) Detecting and measuring genetic differentiation. In: Crustacean Issues: Phylogeography and Population Genetics in Crustacea (eds Koenemann S, Held C, Schubart C), pp. 31–55. CRC Press, Boca Raton, FL, USA.
- (2001) The inheritance of genes in mitochondria and chloroplasts: Laws, mechanisms, and models. Annual Review Genetics, 35, 125–148.
- , , (1989) Organelle gene diversity under migration, mutation, and drift: Equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics, 121, 613–627.
- , (1997) Phylogeography of the sardines (Sardinops spp.): assessing biogeographic models and population histories in temperate upwelling zones. Evolution, 51, 1601–1610.
- , , , (2005) Conservation implications of complex population structure: lessons from the loggerhead turtle (Caretta caretta). Molecular Ecology, 14, 2389–2402.
- , , , , (1995) The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics, 140, 783–796.
- , , , (2006) Effects of Pliestocene glaciations on population structure of North American chestnut-backed chickadees. Molecular Ecology, 15, 2409–2419.
- , , , , (2010) Multiple ice-age refugia in Pacific cod, Gadus macrocephalus. Molecular Ecology, 19, 4339–4351.
- , (2008) Intraspecific phylogeographic genomics from multiple complete mtDNA genomes in Atlantic cod (Gadus morhua): origins of the “codmother,” transatlantic vicariance and midglacial population expansion. Genetics, 180, 381–389.
- (2010) Don’t forget the ancestral polymorphisms. Heredity, 105, 509–510.
- , , et al. (2005) An introduction to the geology of the Bocas del Toro Archipelago, Panama. Caribbean Journal of Science, 41, 374–391.
- , , et al. (2001) Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature, 409, 704–707.
- , , et al. (2012) Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf following the last glacial maximum. Molecular Biology and Evolution, 29, 707–719. Advance Access.
- (1964) Space, Time, Form: The Biological Synthesis. Published by the author, Caracas, Venezuela.
- , , (2005) Variation in mitochondrial DNA and microsatellite DNA in Caribou (Rangifer tarandus) in North American. Journal of Mammalogy, 86, 495–505.
- , (1984) Group selection for polygenic behavioral trait: estimating the degree of population subdivision. Proceedings of the National Academy of Science USA, 81, 6073–6077.
- (1999) A History of Inverse Probability from Thomas Bayes to Karl Pearson, 2nd edn. Springer-Verlag New York, Inc. NY, New York, pp. 15.
- , , et al. (2012) Global phylogeography with mixed marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini). PLoS ONE, 7, e29986. doi:10.1371/journal.pone.0029986
- , , , , (2008) Genetic patterns across multiple introductions of the globally invasive crab genus Carcinus. Molecular Ecology, 17, 4992–5007.
- , , , , (2006) Genetic divergence and migration patterns in a North American passerine bird: implications for evolution and conservation. Molecular Ecology, 15, 2141–2152.
- , , (2008) The evolutionary implications of non-neutral mitochondrial genetic variation. Trends in Ecology and Evolution, 23, 546–554.
- , (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
- , , , , , (2011) Escaping paradise: Larval export from Hawaii in an Indo-Pacific reef fish, the Yellow Tang (Zebrasoma flavescens). Marine Ecology Progress Series, 428, 245–258.
- , , et al. (2010) Conservation genetics of the alligator snapping turtle: cytonuclear evidence of range-wide bottleneck effects and unusually pronounced geographic structure. Conservation Genetics, 11, 1375–1387.
- (2007) Alarm bells for the molecular clock? No support for Ho et al.‘s model of time-dependent molecular rate estimates. Systematic Biology, 56, 337–345.
- , , (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Molecular Ecology, 11, 1591–1604.
- , , (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1, 47–50.
- , , (2008) A reevaluation of the Native American mtDNA genome diversity and its bearing on the models of early colonization. PLoS ONE, 3, e3157.
- , , (2007) Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates. Molecular Ecology, 16, 1149–1166.
- , (1999) A human population bottleneck can account for the discordance between patterns of mitochondrial and nuclear DNA variation. Molecular Biology and Evolution, 16, 1003–1005.
- (2006) Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? Molecular Biology and Evolution, 23, 691–700.
- , , et al. (2011) High connectivity in the deepwater snapper Pristipomoides filamentosus (Lutjanidae) across the Indo-Pacific with isolation of the Hawaiian Archipelago. PLoS ONE, 6, e28913. doi:10.1371/journal.pone.0028913.
- , , , , (2006) Homoploid hybrid speciation in an extreme habitat. Science, 314, 1923–1925.
- , (2012) Incorporating deep and shallow components of genetic structure into the management of Alaskan red king crab. Evolutionary Applications, in press.
- , , et al. (2008) A phylogenomic study of birds revels their evolutionary history. Science, 320, 1763–1769.
- , (2001) Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proceedings of the Royal Scoiety, London, Series B, 268, 939–945.
- , , et al. (2008) Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences, USA, 105, 13462–13467.
- (1999) Highly variable loci and their interpretation in evolution and conservation. Evolution, 53, 313–318.
- , (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics, 167, 747–760.
- , , (2003) Calibrating a molecular clock from phylogeographic data: moments and likelihood estimators. Evolution, 57, 2216–2225.
- , (2006) Molecular clocks: when times are a-changin’. Trends in Genetics, 22, 79–83.
- , , , (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution, 22, 1561–1568.
- , , , , (2008) The effect of inappropriate calibration: three case studies in molecular ecology. PLoS ONE, 3, e1615.
- , , et al. (2011) Time-dependent rates of molecular evolution. Molecular Ecology, 20, 3087–3101.
- , , , , (2007) Glacial refugia and recolonization pathways in the brown seaweed Fucus serratus. Molecular Ecology, 16, 3606–3616.
- , , et al. (2010) Population genomics of parallel adaptation in Threespine Stickleback using sequenced RAD tags. PLoS Genetics, 6, e1000862. doi:10.1371/journal.pgen.1000862.
- , (2009) Genetics in geographically structured populations: defining, estimating and interpreting FST. Nature Reviews Genetics, 10, 639–650.
- , (2006) Nonneutral evolution of organelle genes in Silene vulgaris. Genetics, 174, 1983–1994.
- (1943) untitled. American Naturalist, 77, 365–368.
- (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology, 7, 1–44.
- (1943) Evolution: The Modern Synthesis. Harper and Brothers, New York, NY.
- , , et al. (2007) Orbital and millennial Antarctic climate variability over the past 800,000 years. Science, 317, 793–797.
- , , (1989) The “hitchhiking effect” revised. Genetics, 123, 887–899.
- , , (1992) Global population structure and male-mediated gene flow in the green turtle (Chelonia mydas): RFLP analysis of anonymous nuclear loci. Genetics, 131, 163–173.
- , , et al. (2005) Microsatellite and mitochondrial DNA analyses of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern Atlantic, Gulf of Mexico, and Caribbean Sea. Molecular Ecology, 14, 1911–1923.
- , , (2002) Extreme sex-biased dispersal in the communally breeding, nonmigratory Bechstein’s bat (Myotis bechsteinii). Molecular Ecology, 11, 1491–1498.
- , (2004) Linkage disequilibrium as a signature of selective sweeps. Genetics, 167, 1513–1524.
- , (2002) Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics, 160, 765–777.
- (1943) The great biological generalization. The Quarterly Review of Biology, 18, 364–367.
- , , , (2010) Bayesian Analysis for Population Ecology. CRC Press, New York, NY.
- (1982) The coalescent. Stochastic Processes and their Applications, 13, 235–248.
- , , (2008) A three-stage colonization model for the peopling of the Americas. PLoS ONE, 3, e1596.
- , , (2002) Links between climate and sea levels for the past three million years. Nature, 419, 199–206.
- , , , , (2002) Microsatellite DNA and mitochondrial DNA variation in remnant and translocated sea otter (Enhydra lutris) populations. Journal of Mammalogy, 83, 893–906.
- , , , (2009) Statistical power for detecting divergence – organelle versus nuclear markers. Conservation Genetics, 10, 1255–1264.
- , (1966) A molecular approach to the study of genetic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics, 54, 595–605.
- , (2007) Mitonuclear discordance is caused by rampant mitochondrial introgression in Neodiprion (Hymenoptera: Diprionidae) sawflies. Evolution, 61, 1417–1438.
- , , , , (2010) Remarkably low mtDNA control-region diversity and shallow population structure in Pacific cod Gadus macrocephalus. Journal of Fish Biology, 77, 1071–1082.
- , , (2001) Contrasting patterns of mitochondrial DNA and microsatellite introgressive hybridization between lineages of lake whitefish (Coregonus clupeaformis); relevance for speciation. Molecular Ecology, 10, 965–985.
- , , et al. (1999) Sex-biased dispersal in sperm whales: contrasting mitochondrial and nuclear genetic structure of global populations. Proceedings of the Royal Society of London Series B, 266, 347–354.
- (2002) Fossil calibration of molecular clocks and the divergence time of geminate species pairs separated by the Isthmus of Panama. Molecular Biology and Evolution, 19, 2005–2021.
- , (2009) Out of sight, out of mind: high cryptic diversity obscures the identities and histories of geminate species in the marine bivalve subgenus Acar. Journal of Biogeography, 36, 1861–1880.
- , , et al. (2009) In the academic job market, will you be competitive? A case study in ecology and evolutionary biology. Israel Journal of Ecology & Evolution, 55, 381–392.
- , (1977) A new method for sequencing DNA. Proceedings of the National Academy of Science USA, 74, 560–564.
- , (1974) The hitch-hiking effect of a favourable gene. Genetic Research, 23, 23–35.
- , (2010) Positive relationship between genetic diversity and abundance in fishes. Molecular Ecology, 19, 4852–4862.
- , (2001) Resolution of population structure in a species with high gene flow: microsatellite variation in the eulachon (Osmeridae: Thaleichthys pacificus). Marine Biology, 139, 411–420.
- , (2011) Assessing population structure: FST and related measures. Molecular Ecology Resources, 11, 5–18.
- , , (2006) Comment on “population size does not influence mitochondrial genetics diversity in animals”. Science, 314, 1390.
- , , , , (2011) The evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation. BMC Evolutionary Biology, 11, 177.
- , , (1975) The bottleneck effect and genetic variability in populations. Evolution, 29, 1–10.
- (2010) Quality and peer review of research: an adjudicating role for editors. Accountability in Research, 17, 130–145.
- (2005) Molecular signatures of natural selection. Annual Review of Genetics, 39, 197–218.
- (2001) From the editors. The Academy of Management Journal, 44, 1079–1080.
- , , , (1998) Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature, 396, 572–575.
- , , , (2004) Inverse relationship between FST and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure. Molecular Ecology, 13, 1799–1814.
- , , (2001) Should auld acquaintance be forgot: Possible influence of computer databases on citation patterns in the biological literature. BioScience, 51, 583–588.
- , , , (2007) Testing hypotheses of population structuring in the Northeast Atlantic Ocean and Mediterranean Sea using the common cuttlefish Sepia officinalis. Molecular Ecology, 16, 2667–2679.
- , , et al. (2005) Climate change and distribution shifts in marine fishes. Science, 308, 1912–1915.
- , (2009) Quantitative prediction of molecular clock and Ka/Ks at short timescales. Molecular Biology and Evolution, 26, 2595–2603.
- , , , (2010) Tinamous and Moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Systematic Biology, 59, 90–107.
- , , et al. (2000) Matrilineal genetic structure and female mediated gene flow in the red grouse (Lagopus lagopus scoticus): an analysis using mitochondrial DNA. Evolution, 54, 279–289.
- , , , (1976) Evolution of flightless land birds on southern continents—transferrin comparison shows monophyletic origin of ratites. Journal of Molecular Evolution, 8, 283–294.
- , , (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.
- , (2002) Inferring sex-biased dispersal from population genetic tools: a review. Heredity, 88, 161–165.
- , (1996) Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Molecular Ecology and Evolution, 13, 735–748.
- , , , , (2010) Conflicting patterns of nucleotide diversity between mtDNA and nDNA in the Moorish gecko, Tarentola mauritanica. Molecular Phylogenetics and Evolution, 56, 962–971.
- , (1995) GENEPOP (version 3.3): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248–249.
- , (1992) Population growth makes waves in the distribution of pairwise differences. Molecular Biology and Evolution, 9, 552–569.
- , , , , (2001) Understanding patterns of genetic diversity in the oak gallwasp Biorhiza pallida: demographic history or a Wolbachia selective sweep? Heredity, 87, 294–304.
- , , , (1999) Cryptic evolution and population structure of the alligator snapping turtle, Macroclemys temminckii. Conservation Biology, 13, 135–142. Direct Link:
- , (2003) MrBAyes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572–1574.
- , (2002) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics, 3, 380–390.
- , (2006) POWSIM: a computer program for assessing statistical power when testing for genetic differentiation. Molecular Ecology Notes, 6, 600–602.
- , , et al. (2006) Power for detecting genetic divergence: differences between statistical methods and marker loci. Molecular Ecology, 15, 231–245.
- , , , , (2000) mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. American Journal of Human Genetics, 67, 718–726.
- , (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology, 94, 441–448.
- , , , (2001) Patterns of mtDNA and microsatellite variation in an island and mainland population of guanacos in southern Chile. Animal Conservation, 4, 93–101.
- , (2011) High rate of calculation errors in mismatch distribution analysis results in numerous false inferences of biological importance. Heredity, 107, 511–512.
- (2004) The evolution of molecular markers – just a matter of fashion. Nature Reviews Genetics, 5, 63–70.
- (1943) untitled. Copeia, 1943, 262–263.
- , (2009) The peer-review and editorial system: ways to fix something that might be broken. Perspectives on Psychological Science, 4, 54–61. Direct Link:
- , , et al. (2001) Sex-biased gene flow in spectacled eider (Anatidae): inference from molecular markers with contrasting modes of inheritance. Evolution, 55, 2105–2115.
- , , (1998) Genetic evidence for a higher female migration rate in humans. Nature Genetics, 20, 278–280.
- , (1969) Protein polymorphism and genic heterozygosity in a wild population of the house mouse (Mus musculus). Genetics, 63, 653–667.
- , (1990) Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press, New Haven CT.
- (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution, 47, 264–279.
- (1997) Peer review: reform or revolution? BMJ, 315, 759.
- , , , (2004) Mitochondrial DNA variation in northeast Atlantic and Mediterranean populations of Norway lobster, Nephrops norvegicus. Molecular Ecology, 13, 1377–1390.
- , (2009) Limited genetic variation and structure in softshell clams (Mya arenaria) across their native and introduced range. Conservation Genetics, 10, 803–814.
- , (1981) BIOSYS-1: a FORTRAN program for the comprehensive analysis of electrophoretic data in population genetics and systematics. Journal of Heredity, 72, 281–283.
- , (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512–526.
- , , et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739.
- , , et al. (2008) High connectivity on a global scale in the pelagic wahoo, Acanthocybium solandri (tuna family Scombridae). Molecular Ecology, 17, 4233–4247.
- (2005) Foundations of gregariousness in barnacles. Journal of Experimental Biology, 208, 1773–1774.
- , (2007) The as-is journal review process: Let authors own their ideas. Academy of Management Learning and Education, 6, 128–136.
- , (1991) Rapid spread of an inherited incompatibility factor in California Drosophila. Nature, 353, 440–442.
- , , (1973) Genetic variability and relationships in Pacific salmon and related trout based on protein variations. Systematic Zoology, 22, 257–270.
- , , , (2011) A new age model for the Pliocene-Pleistocene Tjörnes section on Iceland: Its implication for the timing of North Atlantic-Pacific palaeoceanographic pathways. Palaeogeography, Palaeoclimatology, Palaeoecology, 309, 33–52.
- , , (2010) No crisis in supply of peer reviewers. Nature, 468, 1041.
- , , , , (2011) Azooxanthellate? Most Hawaiian black corals contain Symbiodinium. Proceedings of the Royal Society B: Biological Sciences, 278, 1323–1328.
- , (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology, 15, 1419–1439.
- , , , , (2006) Mitochondrial DNA and population size. Science, 314, 1388–1390.
- (1990) The human genome project: past, present & future. Science, 248, 44–49.
- , (1999) Indirect measures of gene flow and migration: Fst ≠ 1(4Nm + 1). Heredity, 82, 117–125.
- (1943) Isolation by distance. Genetics, 28, 139–156.
- (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution, 19, 395–420.

1365-294X/asset/MEC_centre.gif?v=1&s=a3addb330bee9658564df3325c89548d75a4238d)
