High Rate of Calculation Errors in Mismatch Distribution Analysis Result in Numerous False

High rate of calculation errors in mismatch distribution analysis result in numerous false inferences of biological importance

T. SCHENEKAR and S. WEISS

Supplementary File II

List 1: Manuscripts that reported a time since expansion value that matched our re-calculation or fell within the ± 5% tolerance interval

Almada VC, Pereira AM, Robalo JI, et al. (2008) Mitochondrial DNA fails to reveal genetic structure in sea-lampreys along European shores. Mol Phylogenet Evol 46, 391-396.

Alvarez-Castaneda ST, Patton JL (2004) Geographic genetic architecture of pocket gopher (Thomomys bottae) populations in Baja California, Mexico. Mol Ecol 13, 2287-2301.

Ascunce MS, Hasson E, Mulligan CJ, Mudry MD (2007) Mitochondrial sequence diversity of the southernmost extant New World monkey, Alouatta caraya. Mol Phylogenet Evol 43, 202-215.

Baker AM, Williams SA, Hughes JM (2003) Patterns of spatial genetic structuring in a hydropsychid caddisfly (Cheumatopsyche sp. AV1) from southeastern Australia. Mol Ecol 12, 3313-3324.

Boulet M, Gibbs HL (2006) Lineage origin and expansion of a Neotropical migrant songbird after recent glaciation events. Mol Ecol 15, 2505-2525.

Brandli L, Handley LJ, Vogel P, Perrin N (2005) Evolutionary history of the greater white-toothed shrew (Crocidura russula) inferred from analysis of mtDNA, Y, and X chromosome markers. Mol Phylogenet Evol 37, 832-844.

Carlsson J, McDowell JR, Diaz-Jaimes P, et al. (2004) Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea. Mol Ecol 13, 3345-3356.

Chen SF, Rossiter SJ, Faulkes CG, Jones G (2006) Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros). Mol Ecol 15, 1643-1656.

Chu JH, Lin YS, Wu HY (2007) Evolution and dispersal of three closely related macaque species, Macaca mulatta, M. cyclopis, and M. fuscata, in the eastern Asia. Mol Phylogenet Evol 43, 418-429.

Dalen L, Fuglei EVA, et al. (2005) Population history and genetic structure of a circumpolar species: the arctic fox. Biological Journal of the Linnean Society 84, 79-89.

De Gelas K, De Meester L (2005) Phylogeography of Daphnia magna in Europe. Mol Ecol 14, 753-764.

Dejong RJ, Morgan JA, Wilson WD, et al. (2003) Phylogeography of Biomphalaria glabrata and B. pfeifferi, important intermediate hosts of Schistosoma mansoni in the New and Old World tropics. Mol Ecol 12, 3041-3056.

Fedorov VB, Goropashnaya AV, Jaarola M, Cook JA (2003) Phylogeography of lemmings (Lemmus): no evidence for postglacial colonization of Arctic from the Beringian refugium. Mol Ecol 12, 725-731.

Förster DW, Gündüz I, Nunes AC, et al. (2009) Molecular insights into the colonization and chromosomal diversification of Madeiran house mice. Molecular Ecology 18, 4477-4494.

Galbreath KE, Cook JA (2004) Genetic consequences of Pleistocene glaciations for the tundra vole (Microtus oeconomus) in Beringia. Molecular Ecology 13, 135-148.

García JT, Suárez F, Garza V, et al. (2008) Genetic and phenotypic variation among geographically isolated populations of the globally threatened Dupont's lark Chersophilus duponti. Molecular Phylogenetics and Evolution 46, 237-251.

Gelembiuk GW, May GE, Lee CE (2006) Phylogeography and systematics of zebra mussels and related species. Mol Ecol 15, 1033-1050.

Goropashnaya AV, Fedorov VB, Seifert B, Pamilo P (2004) Limited phylogeographical structure across Eurasia in two red wood ant species Formica pratensis and F. lugubris (Hymenoptera, Formicidae). Mol Ecol 13, 1849-1858.

Gysels ES, Hellemans B, Pampoulie C, Volckaert FA (2004a) Phylogeography of the common goby, Pomatoschistus microps, with particular emphasis on the colonization of the Mediterranean and the North Sea. Mol Ecol 13, 403-417.

Hasan AU, Suguri S, Fujimoto C, et al. (2008) Phylogeography and dispersion pattern of Anopheles farauti senso stricto mosquitoes in Melanesia. Mol Phylogenet Evol 46, 792-800.

Huang S, He S, Peng Z, Zhao K, Zhao E (2007a) Molecular phylogeography of endangered sharp-snouted pitviper (Deinagkistrodon acutus; Reptilia, Viperidae) in Mainland China. Mol Phylogenet Evol 44, 942-952.

Huang Z, Liu N, Liang W, et al. (2010) Phylogeography of Chinese bamboo partridge, Bambusicola thoracica thoracica (Aves: Galliformes) in south China: inference from mitochondrial DNA control-region sequences. Mol Phylogenet Evol 56, 273-280.

Huang Z, Liu N, Luo S, Long J (2007b) Phylogeography of rusty-necklaced partridge (Alectoris magna) in northwestern China. Mol Phylogenet Evol 43, 379-385.

Hull JM, Girman DJ (2005) Effects of Holocene climate change on the historical demography of migrating sharp-shinned hawks (Accipiter striatus velox) in North America. Mol Ecol 14, 159-170.

Hundertmark KJ, Shields GF, Udina IG, et al. (2002) Mitochondrial phylogeography of moose (Alces alces): late pleistocene divergence and population expansion. Mol Phylogenet Evol 22, 375-387.

Ishida S, Taylor DJ (2007) Quaternary diversification in a sexual Holarctic zooplankter, Daphnia galeata. Mol Ecol 16, 569-582.

Johannesen JES, Kiefer A, Veith M, Kral J (2005) Genetic cohesion of Eresus walckenaeri (Araneae, Eresidae) in the eastern Mediterranean. Biological Journal of the Linnean Society 86, 1-9.

Johnson JA, Dunn PO, Bouzat JL (2007) Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickens. Mol Ecol 16, 2203-2222.

Jolly MT, Viard F, Gentil F, Thiebaut E, Jollivet D (2006) Comparative phylogeography of two coastal polychaete tubeworms in the Northeast Atlantic supports shared history and vicariant events. Mol Ecol 15, 1841-1855.

Joseph L, Wilke T, Alpers D (2002) Reconciling genetic expectations from host specificity with historical population dynamics in an avian brood parasite, Horsfield's Bronze-Cuckoo Chalcites basalis of Australia. Mol Ecol 11, 829-837.

Koskinen MT, Knizhin I, Primmer CR, Schlotterer C, Weiss S (2002) Mitochondrial and nuclear DNA phylogeography of Thymallus spp (grayling) provides evidence of ice-age mediated environmental perturbations in the world's oldest body of fresh water, Lake Baikal. Mol Ecol 11, 2599-2611.

Kvist L, Broggi J, Illera JC, Koivula K (2005) Colonisation and diversification of the blue tits (Parus caeruleus teneriffae-group) in the Canary Islands. Mol Phylogenet Evol 34, 501-511.

Lebarbenchon C, Poitevin F, Arnal V, Montgelard C (2010) Phylogeography of the weasel (Mustela nivalis) in the western-Palaearctic region: combined effects of glacial events and human movements. Heredity.

Lecomte F, Grant WS, Dodson JJ, Rodriguez-Sanchez R, Bowen BW (2004) Living with uncertainty: genetic imprints of climate shifts in East Pacific anchovy (Engraulis mordax) and sardine (Sardinops sagax). Mol Ecol 13, 2169-2182.

Lindblom L, Ekman S (2006) Genetic variation and population differentiation in the lichen-forming ascomycete Xanthoria parietina on the island Storfosna, central Norway. Mol Ecol 15, 1545-1559.

Liu JX, Gao TX, Yokogawa K, Zhang YP (2006a) Differential population structuring and demographic history of two closely related fish species, Japanese sea bass (Lateolabrax japonicus) and spotted sea bass (Lateolabrax maculatus) in Northwestern Pacific. Mol Phylogenet Evol 39, 799-811.

Liu JX, Gao TX, Zhuang ZM, et al. (2006b) Late Pleistocene divergence and subsequent population expansion of two closely related fish species, Japanese anchovy (Engraulis japonicus) and Australian anchovy (Engraulis australis). Mol Phylogenet Evol 40, 712-723.

Liu Y, Zhan X, Wang N, Chang J, Zhang Z (2010) Effect of geological vicariance on mitochondrial DNA differentiation in Common Pheasant populations of the Loess Plateau and eastern China. Mol Phylogenet Evol 55, 409-417.

Ludwig A, Congiu L, Pitra C, et al. (2003) Nonconcordant evolutionary history of maternal and paternal lineages in Adriatic sturgeon. Mol Ecol 12, 3253-3264.

Malyarchuk B, Derenko M, Berman D, et al. (2010) Phylogeography and molecular adaptation of Siberian salamander Salamandrella keyserlingii based on mitochondrial DNA variation. Mol Phylogenet Evol 56, 562-571.

Mareile Techow NM, Ryan PG, O'Ryan C (2009) Phylogeography and taxonomy of White-chinned and Spectacled Petrels. Mol Phylogenet Evol 52, 25-33.

Marko PB, Hoffman JM, Emme SA, et al. (2010) The ‘Expansion–Contraction’ model of Pleistocene biogeography: rocky shores suffer a sea change? Molecular Ecology 19, 146-169.

Marmi J, Bertranpetit J, Terradas J, Takenaka O, Domingo-Roura X (2004) Radiation and phylogeography in the Japanese macaque, Macaca fuscata. Mol Phylogenet Evol 30, 676-685.

McMillen-Jackson AL, Bert TM (2003) Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species (Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States. Mol Ecol 12, 2895-2905.

Melo-Ferreira J, Boursot P, Randi E, et al. (2007) The rise and fall of the mountain hare (Lepus timidus) during Pleistocene glaciations: expansion and retreat with hybridization in the Iberian Peninsula. Mol Ecol 16, 605-618.

Navascues M, Vaxevanidou Z, Gonzalez-Martinez SC, et al. (2006) Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine. Mol Ecol 15, 2691-2698.

Ostbye K, Bernatchez L, Naesje TF, Himberg KJ, Hindar K (2005) Evolutionary history of the European whitefish Coregonus lavaretus (L.) species complex as inferred from mtDNA phylogeography and gill-raker numbers. Mol Ecol 14, 4371-4387.

Pedraza-Lara C, Alda F, Carranza S, Doadrio I (2010) Mitochondrial DNA structure of the Iberian populations of the white-clawed crayfish, Austropotamobius italicus italicus (Faxon, 1914). Mol Phylogenet Evol 57, 327-342.

Peters JL, Gretes W, Omland KE (2005) Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the 'isolation with migration' coalescent method. Mol Ecol 14, 3407-3418.

Pfeiler E, Bitler BG, Castrezana S, Matzkin LM, Markow TA (2009) Genetic diversification and demographic history of the cactophilic pseudoscorpion Dinocheirus arizonensis from the Sonoran Desert. Mol Phylogenet Evol 52, 133-141.

Provan J, Wattier RA, Maggs CA (2005) Phylogeographic analysis of the red seaweed Palmaria palmata reveals a Pleistocene marine glacial refugium in the English Channel. Mol Ecol 14, 793-803.

Qiu YX, Guan BC, Fu CX, Comes HP (2009) Did glacials and/or interglacials promote allopatric incipient speciation in East Asian temperate plants? Phylogeographic and coalescent analyses on refugial isolation and divergence in Dysosma versipellis. Mol Phylogenet Evol.

Qu J, Liu N, Bao X, Wang X (2009) Phylogeography of the ring-necked pheasant (Phasianus colchicus) in China. Mol Phylogenet Evol 52, 125-132.

Qu Y, Lei F (2009) Comparative phylogeography of two endemic birds of the Tibetan plateau, the white-rumped snow finch (Onychostruthus taczanowskii) and the Hume's ground tit (Pseudopodoces humilis). Mol Phylogenet Evol.

Quérouil S, Verheyen E, Dillen M, Colyn M (2003) Patterns of diversification in two African forest shrews: Sylvisorex johnstoni and Sylvisorex ollula (Soricidae, Insectivora) in relation to paleo-environmental changes. Molecular Phylogenetics and Evolution 28, 24-37.

Randi E, Tabarroni C, Rimondi S, Lucchini V, Sfougaris A (2003) Phylogeography of the rock partridge (Alectoris graeca). Mol Ecol 12, 2201-2214.

Rocha LA, Robertson DR, Rocha CR, et al. (2005) Recent invasion of the tropical Atlantic by an Indo-Pacific coral reef fish. Mol Ecol 14, 3921-3928.

Ruzzante DE, Walde SJ, Cussac VE, et al. (2006) Phylogeography of the Percichthyidae (Pisces) in Patagonia: roles of orogeny, glaciation, and volcanism. Mol Ecol 15, 2949-2968.

Seki S, Sakanashi M, Kawaji N, Kotaka N (2007) Phylogeography of the Ryukyu robin (Erithacus komadori): population subdivision in land-bridge islands in relation to the shift in migratory habit. Mol Ecol 16, 101-113.

Strasburg JL, Kearney M (2005) Phylogeography of sexual Heteronotia binoei (Gekkonidae) in the Australian arid zone: climatic cycling and repetitive hybridization. Mol Ecol 14, 2755-2772.

Techow NM, O'Ryan C, Phillips RA, et al. (2010) Speciation and phylogeography of giant petrels Macronectes. Mol Phylogenet Evol 54, 472-487.

Uthicke S, Benzie JA (2003) Gene flow and population history in high dispersal marine invertebrates: mitochondrial DNA analysis of Holothuria nobilis (Echinodermata: Holothuroidea) populations from the Indo-Pacific. Mol Ecol 12, 2635-2648.

Van Houdt JK, De Cleyn L, Perretti A, Volckaert FA (2005) A mitogenic view on the evolutionary history of the Holarctic freshwater gadoid, burbot (Lota lota). Mol Ecol 14, 2445-2457.

Van Houdt JK, Hellemans B, Volckaert FAM (2003) Phylogenetic relationships among Palearctic and Nearctic burbot (Lota lota): Pleistocene extinctions and recolonization. Molecular Phylogenetics and Evolution 29, 599-612.

Vianna JA, Bonde RK, Caballero S, et al. (2006) Phylogeography, phylogeny and hybridization in trichechid sirenians: implications for manatee conservation. Mol Ecol 15, 433-447.

Voje KL, Hemp C, Flagstad O, Saetre GP, Stenseth NC (2009) Climatic change as an engine for speciation in flightless Orthoptera species inhabiting African mountains. Mol Ecol 18, 93-108.

Yang FS, Li YF, Ding X, Wang XQ (2008) Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change. Mol Ecol 17, 5135-5145.

Yang L, Mayden RL, He S (2009) Population Genetic Structure and Geographical Differentiation of the Chinese Catfish Hemibagrus macropterus (Siluriformes, Bagridae): Evidence for Altered Drainage Patterns. Mol Phylogenet Evol.

Yang SJ, Yin ZH, Ma XM, Lei FM (2006) Phylogeography of ground tit (Pseudopodoces humilis) based on mtDNA: evidence of past fragmentation on the Tibetan Plateau. Mol Phylogenet Evol 41, 257-265.

Zane L, Marcato S, Bargelloni L, et al. (2006) Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum. Mol Ecol 15, 4499-4511.

List 2: Manuscripts that reported a time since expansion value outside the ± 5% tolerance interval of our re-calculations

Aboim MA, Menezes GM, Schlitt T, Rogers AD (2005) Genetic structure and history of populations of the deep-sea fish Helicolenus dactylopterus (Delaroche, 1809) inferred from mtDNA sequence analysis. Mol Ecol 14, 1343-1354.

Alpers DL, Van Vuuren BJ, Arctander P, Robinson TJ (2004) Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation. Mol Ecol 13, 1771-1784.

Atarhouch T, Ruber L, Gonzalez EG, et al. (2006) Signature of an early genetic bottleneck in a population of Moroccan sardines (Sardina pilchardus). Mol Phylogenet Evol 39, 373-383.

Babbucci M, Buccoli S, Cau A, et al. (2010) Population structure, demographic history, and selective processes: contrasting evidences from mitochondrial and nuclear markers in the European spiny lobster Palinurus elephas (Fabricius, 1787). Mol Phylogenet Evol 56, 1040-1050.

Bailey NW, Gwynne DT, Ritchie MG (2007) Dispersal differences predict population genetic structure in Mormon crickets. Mol Ecol 16, 2079-2089.

Barluenga M, Meyer A (2004) The Midas cichlid species complex: incipient sympatric speciation in Nicaraguan cichlid fishes? Mol Ecol 13, 2061-2076.

Barluenga M, Meyer A (2005) Old fish in a young lake: stone loach (Pisces: Barbatula barbatula) populations in Lake Constance are genetically isolated by distance. Mol Ecol 14, 1229-1239.

Bartish IV, Kadereit JW, Comes HP (2006) Late Quaternary history of Hippophae rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (Chsi) sequences and chloroplast DNA variation. Mol Ecol 15, 4065-4083.