Laurin M. How Vertebrates Left Water. Berkeley: University of California Press; 2010.
Book
Google Scholar
Little C. The Terrestrial Invasion: An Ecophysiological Approach to the Origins of Land Animals. Cambridge: Cambridge University Press; 1990.
Google Scholar
Zapata F, Wilson NG, Howison M, Andrade SC, Jorger KM, Schrödl M, et al. Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proc Biol Sci. 2014;281(1794):20141739.
Article
PubMed
PubMed Central
Google Scholar
Kameda Y, Kato M. Terrestrial invasion of pomatiopsid gastropods in the heavy-snow region of the Japanese Archipelago. BMC Evol Biol. 2011;11:118.
Article
PubMed
PubMed Central
Google Scholar
Jörger KM, Stoger I, Kano Y, Fukuda H, Knebelsberger T, Schrödl M. On the origin of Acochlidia and other enigmatic euthyneuran gastropods, with implications for the systematics of Heterobranchia. BMC Evol Biol. 2010;10:323.
Article
PubMed
PubMed Central
Google Scholar
Kano Y, Neusser TP, Fukumori H, Jörger KM, Schrödl M. Sea-slug invasion of the land. Biol J Linn Soc. 2015;116(2):253–9.
Article
Google Scholar
Klussmann-Kolb A, Dinapoli A, Kuhn K, Streit B, Albrecht C. From sea to land and beyond--new insights into the evolution of euthyneuran Gastropoda (Mollusca). BMC Evol Biol. 2008;8:57.
Article
PubMed
PubMed Central
Google Scholar
Romero PE, Pfenninger M, Kano Y, Klussmann-Kolb A. Molecular phylogeny of the Ellobiidae (Gastropoda: Panpulmonata) supports independent terrestrial invasions. Mol Phylogenet Evol. 2016;97:43–54.
Article
PubMed
Google Scholar
Faddeeva A, Studer RA, Kraaijeveld K, Sie D, Ylstra B, Marien J, et al. Collembolan transcriptomes highlight molecular evolution of hexapods and provide clues on the adaptation to terrestrial life. PLoS One. 2015;10(6), e0130600.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vandebergh W, Bossuyt F. Radiation and functional diversification of alpha keratins during early vertebrate evolution. Mol Biol Evol. 2012;29(3):995–1004.
Article
CAS
PubMed
Google Scholar
Nikaido M, Noguchi H, Nishihara H, Toyoda A, Suzuki Y, Kajitani R, et al. Coelacanth genomes reveal signatures for evolutionary transition from water to land. Genome Res. 2013;23(10):1740–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Amemiya CT, Alfoldi J, Lee AP, Fan S, Philippe H, Maccallum I, et al. The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013;496(7445):311–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
George D, Blieck A. Rise of the earliest tetrapods: an early Devonian origin from marine environment. PLoS One. 2011;6(7), e22136.
Article
CAS
PubMed
PubMed Central
Google Scholar
da Fonseca RR, Johnson WE, O’Brien SJ, Ramos MJ, Antunes A. The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics. 2008;9(1):119.
Article
PubMed
PubMed Central
Google Scholar
Moreno-Loshuertos R, Acin-Perez R, Fernandez-Silva P, Movilla N, Perez-Martos A, de Rodriguez C, et al. Differences in reactive oxygen species production explain the phenotypes associated with common mouse mitochondrial DNA variants. Nat Genet. 2006;38(11):1261–8.
Article
CAS
PubMed
Google Scholar
Dalziel AC, Moyes CD, Fredriksson E, Lougheed SC. Molecular evolution of cytochrome c oxidase in high-performance fish (teleostei: Scombroidei). J Mol Evol. 2006;62(3):319–31.
Article
CAS
PubMed
Google Scholar
Garvin MR, Bielawski JP, Sazanov LA, Gharrett AJ. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. J Zool Syst Evol Res. 2015;53(1):1–17.
Article
Google Scholar
Pfenninger M, Lerp H, Tobler M, Passow C, Kelley JL, Funke E, et al. Parallel evolution of cox genes in H2S-tolerant fish as key adaptation to a toxic environment. Nat Commun. 2014;5:3873.
Article
CAS
PubMed
Google Scholar
Garvin MR, Bielawski JP, Gharrett AJ. Positive Darwinian selection in the piston that powers proton pumps in complex I of the mitochondria of Pacific salmon. PLoS One. 2011;6(9), e24127.
Article
CAS
PubMed
PubMed Central
Google Scholar
McClellan DA, Palfreyman EJ, Smith MJ, Moss JL, Christensen RG, Sailsbery JK. Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins. Mol Biol Evol. 2005;22(3):437–55.
Article
CAS
PubMed
Google Scholar
Stoger I, Schrodl M. Mitogenomics does not resolve deep molluscan relationships (yet?). Mol Phylogenet Evol. 2013;69(2):376–92.
Article
CAS
PubMed
Google Scholar
White TR, Conrad MM, Tseng R, Balayan S, Golding R, de Frias Martins AM, et al. Ten new complete mitochondrial genomes of pulmonates (Mollusca: Gastropoda) and their impact on phylogenetic relationships. BMC Evol Biol. 2011;11:295.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grande C, Templado J, Zardoya R. Evolution of gastropod mitochondrial genome arrangements. BMC Evol Biol. 2008;8:61.
Article
PubMed
PubMed Central
Google Scholar
Kocot KM, Halanych KM, Krug PJ. Phylogenomics supports Panpulmonata: opisthobranch paraphyly and key evolutionary steps in a major radiation of gastropod molluscs. Mol Phylogenet Evol. 2013;69(3):764–71.
Article
PubMed
Google Scholar
Schrödl M, Jörger KM, Klussmann-Kolb A, Wilson NG. Bye bye “Opisthobranchia”! A review on the contribution of mesopsammin sea slugs to euthyneuran systematics. Thalassas. 2011;27:101–12.
Google Scholar
Göbbeler K, Klussmann-Kolb A. Out of Antarctica?--new insights into the phylogeny and biogeography of the Pleurobranchomorpha (Mollusca, Gastropoda). Mol Phylogenet Evol. 2010;55(3):996–1007.
Article
PubMed
Google Scholar
Medina M, Lal S, Valles Y, Takaoka TL, Dayrat BA, Boore JL, et al. Crawling through time: transition of snails to slugs dating back to the Paleozoic, based on mitochondrial phylogenomics. Mar Genomics. 2011;4(1):51–9.
Article
PubMed
Google Scholar
Wägele H, Klussmann-Kolb A, Verbeek E, Schrödl M. Flashback and foreshadowing-a review of the taxon Opisthobranchia. Organisms Div Evol. 2014;14(1):133–49.
Article
Google Scholar
Dayrat B, Conrad M, Balayan S, White TR, Albrecht C, Golding R, et al. Phylogenetic relationships and evolution of pulmonate gastropods (Mollusca): new insights from increased taxon sampling. Mol Phylogenet Evol. 2011;59(2):425–37.
Article
PubMed
Google Scholar
Schrödl M. Time to say “Bye-bye Pulmonata”? Spixiana. 2014;37(2):161–4.
Google Scholar
Thomaz D, Guiller A, Clarke B. Extreme divergence of mitochondrial DNA within species of pulmonate land snails. Proceedings of the Royal Society B-Biological Sciences. 1996;263(1368):363–8.
Article
CAS
Google Scholar
Hayashi M, Chiba S. Intraspecific diversity of mitochondrial DNA in the land snail Euhadra peliomphala (Bradybaenidae). Biol J Linn Soc. 2000;70(3):391–401.
Article
Google Scholar
Chiba S. Accelerated evolution of land snails Mandarina in the oceanic Bonin Islands: Evidence from mitochondrial DNA sequences. Evolution. 1999;53(2):460–71.
Article
CAS
Google Scholar
Pinceel J, Jordaens K, Backeljau T. Extreme mtDNA divergences in a terrestrial slug (Gastropoda, Pulmonata, Arionidae): accelerated evolution, allopatric divergence and secondary contact. J Evol Biol. 2005;18(5):1264–80.
Article
CAS
PubMed
Google Scholar
Guiller A, Coutellec-Vreto MA, Madec L, Deunff J. Evolutionary history of the land snail Helix aspersa in the Western Mediterranean: preliminary results inferred from mitochondrial DNA sequences. Mol Ecol. 2001;10(1):81–7.
Article
CAS
PubMed
Google Scholar
Pfenninger M, Posada D. Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution. 2002;56(9):1776–88.
Article
PubMed
Google Scholar
Davison A, Clarke B. History or current selection? A molecular analysis of ‘area effects’ in the land snail Cepaea nemoralis. Proceedings of the Royal Society B-Biological Sciences. 2000;267(1451):1399–405.
Article
CAS
PubMed Central
Google Scholar
Dépraz A, Hausser J, Pfenninger M. A species delimitation approach in the Trochulus sericeus/hispidus complex reveals two cryptic species within a sharp contact zone. BMC Evol Biol. 2009;9:171.
Article
PubMed
PubMed Central
Google Scholar
Goodacre SL. Population structure, history and gene flow in a group of closely related land snails: genetic variation in Partula from the Society Islands of the Pacific. Mol Ecol. 2002;11(1):55–68.
Article
PubMed
Google Scholar
Parmakelis A, Kotsakiozi P, Rand D. Animal mitochondria, positive selection and cyto-nuclear coevolution: insights from pulmonates. PLoS One. 2013;8(4), e61970.
Article
CAS
PubMed
PubMed Central
Google Scholar
James JE, Piganeau G, Eyre-Walker A. The rate of adaptive evolution in animal mitochondria. Mol Ecol. 2016;25(1):67–78.
Article
CAS
PubMed
Google Scholar
Wakeley J. The effects of subdivision on the genetic divergence of populations and species. Evolution. 2000;54(4):1092–101.
Article
CAS
PubMed
Google Scholar
Thacker RW, Hadfield MG. Mitochondrial Phylogeny of Extant Hawaiian Tree Snails (Achatinellinae). Mol Phylogen Evol. 2000;16(2):263–70.
Article
CAS
Google Scholar
Romero P, Ramirez R. Intraspecific divergence and DNA barcodes in Systrophia helicycloides (Gastropoda, Scolodontidae). Rev Peru Biol. 2011;18(2):201–8.
Google Scholar
Sauer J, Hausdorf B. Reconstructing the evolutionary history of the radiation of the land snail genus Xerocrassa on Crete based on mitochondrial sequences and AFLP markers. BMC Evol Biol. 2010;10:299.
Article
PubMed
PubMed Central
Google Scholar
Nolan JR, Bergthorsson U, Adema CM. Physella acuta: atypical mitochondrial gene order among panpulmonates (Gastropoda). J Molluscan Stud. 2014;80(4):388–99.
Article
PubMed
PubMed Central
Google Scholar
Pfenninger M, Cordellier M, Streit B. Comparing the efficacy of morphologic and DNA-based taxonomy in the freshwater gastropod genus Radix (Basommatophora, Pulmonata). BMC Evol Biol. 2006;6:100.
Article
PubMed
PubMed Central
Google Scholar
Zhai W, Nielsen R, Goldman N, Yang Z. Looking for Darwin in genomic sequences--validity and success of statistical methods. Mol Biol Evol. 2012;29(10):2889–93.
Article
CAS
PubMed
Google Scholar
Tomasco IH, Lessa EP. The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection. Mol Phylogenet Evol. 2011;61(1):64–70.
Article
PubMed
Google Scholar
Zhang J, Nielsen R, Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 2005;22(12):2472–9.
Article
CAS
PubMed
Google Scholar
Yang Z, dos Reis M. Statistical properties of the branch-site test of positive selection. Mol Biol Evol. 2011;28(3):1217–28.
Article
CAS
PubMed
Google Scholar
Yang Z. Molecular Evolution: A Statistical Approach. Oxford: Oxford University Press; 2014.
Book
Google Scholar
Young JN, Rickaby RE, Kapralov MV, Filatov DA. Adaptive signals in algal Rubisco reveal a history of ancient atmospheric carbon dioxide. Philos Trans R Soc Lond B Biol Sci. 2012;367(1588):483–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gharib WH, Robinson-Rechavi M. The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. Mol Biol Evol. 2013;30(7):1675–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noel B, et al. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun. 2014;5:3657.
Article
PubMed
PubMed Central
Google Scholar
Beckstead WA, Ebbert MT, Rowe MJ, McClellan DA. Evolutionary pressure on mitochondrial cytochrome b is consistent with a role of CytbI7T affecting longevity during caloric restriction. PLoS One. 2009;4(6), e5836.
Article
PubMed
PubMed Central
Google Scholar
Facon B, Machinle E, Pointier JP, David P. Variation in desiccation tolerance in freshwater snails and its consequences for invasion ability. Biol Invasions. 2004;6:283–93.
Article
Google Scholar
Flores-Molina MR, Thomas D, Lovazzano C, Núñez A, Zapata J, Kumar M, et al. Desiccation stress in intertidal seaweeds: Effects on morphology, antioxidant responses and photosynthetic performance. Aquat Bot. 2014;113:90–9.
Article
CAS
Google Scholar
Mittler R. Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci. 2002;7(9):405–10.
Article
CAS
PubMed
Google Scholar
Shen YY, Liang L, Zhu ZH, Zhou WP, Irwin DM, Zhang YP. Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proc Natl Acad Sci U S A. 2010;107(19):8666–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Da Silva C, Tomasco IH, Hoffmann F, Lessa EP. Genes and ecology: accelerated rates of replacement substitutions in the cytochrome b gene of subterranean rodents. The Open Evolution Journal. 2009;3:17–30.
Google Scholar
Caballero S, Duchene S, Garavito MF, Slikas B, Baker CS. Initial evidence for adaptive selection on the NADH subunit Two of freshwater dolphins by analyses of mitochondrial genomes. PLoS One. 2015;10(5), e0123543.
Article
PubMed
PubMed Central
Google Scholar
Pfenninger M, Weigand A, Balint M, Klussmann-Kolb A. Misperceived invasion: the Lusitanian slug (Arion lusitanicus auct. non-Mabille or Arion vulgaris Moquin-Tandon 1855) is native to Central Europe. Evol Appl. 2014;7(6):702–13.
Article
PubMed
PubMed Central
Google Scholar
Weigand AM, Jochum A, Pfenninger M, Steinke D, Klussmann-Kolb A. A new approach to an old conundrum--DNA barcoding sheds new light on phenotypic plasticity and morphological stasis in microsnails (Gastropoda, Pulmonata, Carychiidae). Mol Ecol Resour. 2011;11(2):255–65.
Article
PubMed
Google Scholar
Steinke D, Albrecht C, Pfenninger M. Molecular phylogeny and character evolution in the Western Palaearctic Helicidae s.l. (Gastropoda: Stylommatophora). Mol Phylogenet Evol. 2004;32(3):724–34.
Article
CAS
PubMed
Google Scholar
Feldmeyer B, Hoffmeier K, Pfenninger M. The complete mitochondrial genome of Radix balthica (Pulmonata, Basommatophora), obtained by low coverage shot gun next generation sequencing. Mol Phylogenet Evol. 2010;57(3):1329–33.
Article
CAS
PubMed
Google Scholar
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647–9.
Article
PubMed
PubMed Central
Google Scholar
Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, et al. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69(2):313–9.
Article
PubMed
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56(4):564–77.
Article
CAS
PubMed
Google Scholar
Abascal F, Zardoya R, Telford MJ. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 2010;38:W7–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Williams ST, Foster PG, Littlewood DT. The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny. Gene. 2014;533(1):38–47.
Article
CAS
PubMed
Google Scholar
Lanfear R, Calcott B, Kainer D, Mayer C, Stamatakis A. Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evol Biol. 2014;14:82.
Article
PubMed
PubMed Central
Google Scholar
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22(21):2688–90.
Article
CAS
PubMed
Google Scholar
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008;57(5):758–71.
Article
PubMed
Google Scholar
Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: 2010 Gateway Computing Environments Workshop (GCE). New Orleans: IEEE; 2010. p. 1–8.
Chapter
Google Scholar
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61(3):539–42.
Article
PubMed
PubMed Central
Google Scholar
Rambaut A, Suchard MA, Xie D, Drummond AJ. Tracer v1.6. 2014.
Google Scholar
Douady CJ, Delsuc F, Boucher Y, Doolittle WF, Douzery EJ. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol Biol Evol. 2003;20(2):248–54.
Article
CAS
PubMed
Google Scholar
Leaché AD, Reeder TW. Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches. Syst Biol. 2002;51(1):44–68.
Article
PubMed
Google Scholar
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Merker S, Thomas S, Volker E, Perwitasari-Farajallah D, Feldmeyer B, Streit B, et al. Control region length dynamics potentially drives amino acid evolution in tarsier mitochondrial genomes. J Mol Evol. 2014;79(1–2):40–51.
Article
CAS
PubMed
Google Scholar
Zeileis A, Grothendiek G. zoo: S3 infraestructure for regular and irregular time series. J Stat Softw. 2005;14(6):1–17.
Article
Google Scholar
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586–91.
Article
CAS
PubMed
Google Scholar
Yang Z, Nielsen R, Goldman N, Pedersen AMK. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 2000;155(1):431–49.
CAS
PubMed
PubMed Central
Google Scholar
Woolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA. TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics. 2003;19(5):671–2.
Article
CAS
PubMed
Google Scholar
McClellan DA, McCracken KG. Estimating the influence of selection on the variable aminoacid sites of the cytochrome b protein functional domains. Mol Biol Evol. 2001;18(6):917–25.
Article
CAS
PubMed
Google Scholar
Romero PE, Weigand AM, Pfenninger M. Positive selection on panpulmonate mitogenomes provide new clues on adaptations to terrestrial life. FigShare. 2016. https://dx.doi.org/10.6084/m9.figshare.c.3291377.