Fishes in the desert: mitochondrial variation and phylogeography of Danakilia (Actinopterygii: Cichlidae) and Aphanius (Actinopterygii: Cyprinodontidae) in the Danakil Depression of northeastern Africa

References

• Abbate E, Albianelli A, Azzaroli A, Benvenuti M, Tesfamariam B, Bruni P, Cipriani N, Clarke RJ, Ficcarelli G, Macchiarelli R, et al. 1998. A one-million-year-old Homo cranium from the Danakil (Afar) depression of Eritrea. Nature. 393:458–460.
   PubMed Web of Science ®Google Scholar
• Barberi F, Borsi S, Ferrara G, Marinelli G, Santacroce R, Tazieff H, Varet J. 1972. Evolution of the Danakil Depression (Afar, Ethiopia) in light of radiometric age determinations. J Geol. 80:720–729.
   Web of Science ®Google Scholar
• Bensasson D, Feldman MW, Petrov DA. 2003. Rates of DNA duplication and mitochondrial DNA insertion in the human genome. J Mol Evol. 57:343–354.
   PubMed Web of Science ®Google Scholar
• Beyene A, Abdelsalam MG. 2005. Tectonics of the Afar depression: a review and synthesis. J Afr Earth Sci. 41:41–59.
   Web of Science ®Google Scholar
• Bonatti E, Emiliani C, Ostlund G, Rydell H. 1971. Final desiccation of the Afar rift, Ethiopia. Science. 172:468–469.
   PubMed Web of Science ®Google Scholar
• Buhay JE. 2009. ‘COI-like’ sequences are becoming problematic in molecular systematic and DNA barcoding studies. J Crustacean Biol. 29:96–110.
   Web of Science ®Google Scholar
• Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Mol Ecol. 9:1657–1659.
   PubMed Web of Science ®Google Scholar
• Delfino M, Segid A, Yosief D, Shoshani J, Rook L, Libsekal Y. 2004. Fossil reptiles from the Pleistocene Homo-bearing locality of Buia (Eritrea, northern Danakil Depression). Riv Ital Di Paleontol Stratigrafia (Res Paleontol Stratigraphy). 110:51–60.
   Web of Science ®Google Scholar
• Dunz AR, Schliewen UK. 2013. Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as “Tilapia”. Mol Phylogenet Evol. 68:64–80.
   PubMed Web of Science ®Google Scholar
• Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Mol Ecol. 11:2571–2581.
   PubMed Web of Science ®Google Scholar
• Erdmann MV. 1999. Clove oil: an ‘eco-friendly’ alternative to cyanide use in the live reef fish industry. SPC Live Reef Fish Inform Bull. 5:4–7.
   Google Scholar
• Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform. 1:47–50.
   PubMed Web of Science ®Google Scholar
• Faure H, Walter RC, Grant DR. 2002. The coastal oasis: ice age springs on emerged continental shelves. Glob Planet Change. 33:47–56.
   Web of Science ®Google Scholar
• Ferretti MP, Ficcarelli G, Libsekal Y, Tecle TM, Rook L. 2003. Fossil elephants from Buia (northern Afar Depression, Eritrea) with remarks on the systematics of Elephas recki (Proboscidea, Elephantidae). J Vertebr Paleontol. 23:244–257.
   Web of Science ®Google Scholar
• Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol. 3:294–299.
   PubMedGoogle Scholar
• Franchetti R. 1930. Nella dancalia etiopica. Milano (Italy): Arnoldo Mondadori Editore.
   Google Scholar
• Galván-Quesada S, Doadrio I, Alda F, Perdices A, Reina RG, García Varela M, Hernández N, Campos Mendoza A, Bermingham E, Domínguez-Domínguez O, et al. 2016. Molecular phylogeny and biogeography of the Amphidromous Fish Genus Dormitator Gill 1861 (Teleostei: Eleotridae). PLoS One. 11:e0153538.
   PubMed Web of Science ®Google Scholar
• Gasse F, Street FA. 1978. Late Quaternary lake-level fluctuations and environments of the northern Rift Valley and Afar region (Ethiopia and Djibouti). Palaeogeogr Palaeoclimatol Palaeoecol. 24:279–325.
   Web of Science ®Google Scholar
• Gasse F, Téhet R, Durand A, Gibert E, Fontes JC. 1990. The arid-humid transition in the Sahara and the Sahel during the last deglaciation. Nature. 346:141–146.
   Web of Science ®Google Scholar
• Gasse F. 1974. Les Diatomées des Sédiments Holocènes du Bassin du Lac Afrera (Giulietti) (Afar Septentrional, Ethiopie). Essai de Reconstitution de l'Évolution du Milieu. Int Rev Der Gesamten Hydrobiol Hydrograph. 59:95–122.
   Google Scholar
• Geiger MF, Herder F, Monaghan MT, Almada V, Barbieri R, Bariche M, Berrebi P, Bohlen J, Casal-Lopez M, Delmastro GB, et al. 2014. Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes. Mol Ecol Resour. 14:1210–1221.
   PubMed Web of Science ®Google Scholar
• Getahun A, Lazara KJ. 2001. Lebias stiassnyae: a new species of killifish from Lake Afrera, Ethiopia (Teleostei: Cyprinodontidae). Copeia. 2001:150–153.
   Google Scholar
• Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 41:47–50.
   Google Scholar
• Hebert PD, Ratnasingham S, de Waard JR. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B: Biol Sci. 270:S96–S99.
   PubMed Web of Science ®Google Scholar
• Hillyard SD, Podrabsky JE, van Breukelen F. 2015. Desert environments. In: Riesch R, Tobler M, Plath M, editors. Extremophile fishes: ecology, evolution, and physiology of teleosts in extreme environments. Heidelberg (Germany): Springer International Publishing; p. 59–83.
   Google Scholar
• Hoelzmann P, Jolly D, Harrison SP, Laarif F, Bonnefille R, Pachur HJ. 1998. Mid‐Holocene land‐surface conditions in northern Africa and the Arabian Peninsula: a data set for the analysis of biogeophysical feedbacks in the climate system. Glob Biogeochem Cycl. 12:35–51.
   Web of Science ®Google Scholar
• Hrbek T, Meyer A. 2003. Closing of the Tethys Sea and the phylogeny of Eurasian killifishes (Cyprinodontiformes: Cyprinodontidae). J Evol Biol. 16:17–36.
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Rannala B, Buckley T. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol. 53:904–913.
   PubMed Web of Science ®Google Scholar
• Johns GC, Avise JC. 1998. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Mol Biol Evol. 15:1481–1490.
   PubMed Web of Science ®Google Scholar
• Kleinhans MG, Ferguson RI, Lane SN, Hardy RJ. 2013. Splitting rivers at their seams: bifurcations and avulsion. Earth Surf Process Landforms. 38:47–61.
   Web of Science ®Google Scholar
• Klett V, Meyer A. 2002. What, if anything, is a Tilapia? – mitochondrial ND2 phylogeny of tilapiines and the evolution of parental care systems in the African cichlid fishes. Mol Biol Evol. 19:865–883.
   PubMed Web of Science ®Google Scholar
• Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, Villablanca FX, Wilson AC. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci. 86:6196–6200.
   PubMed Web of Science ®Google Scholar
• Lanfear R, Calcott B, Ho SY, Guindon S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 29:1695–1701.
   PubMed Web of Science ®Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
   PubMed Web of Science ®Google Scholar
• López DL, Williams SN. 1993. Catastrophic volcanic collapse: relation to hydrothermal processes. Science. 260:1794–1796.
   PubMed Web of Science ®Google Scholar
• Lowenstern JB, Janik CJ, Fournier RO, Tesfai T, Duffield WA, Clynne MA, Smith JG, Woldegiorgis L, Weldemariam K, Kahsai G. 1999. A geochemical reconnaissance of the Alid volcanic center and geothermal system, Danakil Depression, Eritrea. Geothermics. 28:161–187.
   Web of Science ®Google Scholar
• Martinez-Navarro B, Rook L, Segid A, Yosief D, Ferretti MP, Shoshani J, Tecle TM, Libsekal Y. 2004. The large fossil mammals from Buia (Eritrea): systematics, biochronology and paleoenvironments. Riv Ital Stratigrafia Paleontol. 110:61–88.
   Web of Science ®Google Scholar
• Martini M. 1969. La geochimica del lago Giulietti (Etiopia). Rendiconti Della Soc Ital Mineral Petrol. 25:65–78.
   Google Scholar
• Mohr P. 1978. Afar. Annu Rev Earth Planet Sci. 6:145–172.
   Web of Science ®Google Scholar
• Nagl S, Tichy H, Mayer WE, Samonte IE, McAndrew BJ, Klein J. 2001. Classification and phylogenetic relationships of African tilapiine fishes inferred from mitochondrial DNA sequences. Mol Phylogenet Evol. 20:361–374.
   PubMed Web of Science ®Google Scholar
• Peakall R, Smouse PE. 2012. GenAlEx Tutorial 3. Spatial genetic analysis; [accessed 2017 Nov 15]. http://biology-assets.anu.edu.au/GenAlEx/Tutorials.html
   Google Scholar
• Pedgley DE. 1967. Air temperature at Dallol, Ethiopia. Meteorol Mag. 96:265–271.
   Web of Science ®Google Scholar
• Polačik M, Podrabsky JE. 2015. Temporary environments. In: Riesch R, Tobler M, Plath M, editors. Extremophile fishes: ecology, evolution, and physiology of teleosts in extreme environments. Heidelberg (Germany): Springer International Publishing; p. 217–245.
   Google Scholar
• Rambaut A, Drummond AJ. 2007. Tracer, version 1.5; [accessed 2017 Nov 15]. http://tree.bio.ed.ac.uk/software/tracer/.
   Google Scholar
• Rambaut A. 2009. FigTree version 1.3.1; [accessed 2017 Nov 15]. http://tree.bio.ed.ac.uk/software/figtree/.
   Google Scholar
• Reichenbacher B, Feulner GR, Schulz‐Mirbach T. 2009. Geographic variation in otolith morphology among freshwater populations of Aphanius dispar (Teleostei, Cyprinodontiformes) from the southeastern Arabian Peninsula. J Morphol. 270:469–484.
   PubMed Web of Science ®Google Scholar
• Rognon P. 1972. Le désert de l'Afar (Ethiopie). Bull L'Assoc Géogr Français. 49:235–249.
   Google Scholar
• Rohling EJ, Fenton M, Jorissen FJ, Bertrand P, Ganssen G, Caulet JP. 1998. Magnitudes of sea-level lowstands of the past 500,000 years. Nature. 394:162–165.
   Web of Science ®Google Scholar
• Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61:539–542.
   PubMed Web of Science ®Google Scholar
• Rook L, Ghinassi M, Carnevale G, Delfino M, Pavia M, Bondioli L, Candilio F, Coppa A, Martinez-Navarro B, Medin T, et al. 2013. Stratigraphic context and paleoenvironmental significance of minor taxa (Pisces, Reptilia, Aves, Rodentia) from the late Early Pleistocene paleoanthropological site of Buia (Eritrea). J Hum Evol. 64:83–92.
   PubMed Web of Science ®Google Scholar
• Rüppell WPES. 1828–1830. Lebias. (Cuv.). Atlas zu der Reise im nördlichen Afrika. Fische des Rothen Meers. Frankfurt am Main: Heinrich Ludwig Brönner; p. 66–67.
   Google Scholar
• Schwarzer J, Shabani N, Esmaeili HR, Mwaiko S, Seehausen O. 2016. Allopatric speciation in the desert: diversification of cichlids at their geographical and ecological range limit in Iran. Hydrobiologia. 791:193–207.
   Web of Science ®Google Scholar
• Seehausen O, Terai Y, Magalhaes IS, Carleton KL, Mrosso HD, Miyagi R, van der Sluijs I, Schneider MV, Maan ME, Tachida H, et al. 2008. Speciation through sensory drive in cichlid fish. Nature. 455:620–626.
   PubMed Web of Science ®Google Scholar
• Shaffer HB, Thomson RC. 2007. Delimiting species in recent radiations. Syst Biol. 56:896–906.
   PubMed Web of Science ®Google Scholar
• Song H, Buhay JE, Whiting MF, Crandall KA. 2008. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci. 105:13486–13491.
   PubMed Web of Science ®Google Scholar
• Stiassny ML, De Marchi G, Lamboj A. 2010. A new species of Danakilia (Teleostei, Cichlidae) from lake abaeded in the Danakil Depression of Eritrea (East Africa). Zootaxa. 2690:43–52.
   Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30:2725–2729.
   PubMed Web of Science ®Google Scholar
• Tazieff H, Marinelli G, Barberi F, Varet J. 1969. Géologie de l’Afar septentrional. Bull Volcanol. 33:1039–1072.
   Google Scholar
• Tazieff H, Varet J, Barberi F, Giglia G. 1972. Tectonic significance of the Afar (or Danakil) depression. Nature. 235:144–147.
   Web of Science ®Google Scholar
• Teimori A, Schulz-Mirbach T, Esmaeili HR, Reichenbacher B. 2012. Geographical differentiation of Aphanius dispar (Teleostei: Cyprinodontidae) from Southern Iran. J Zool Syst Evol Res. 50:289–304.
   Web of Science ®Google Scholar
• Templeton AR, Crandall KA, Sing CF. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics. 132:619–633.
   PubMed Web of Science ®Google Scholar
• Trewavas E. 1983. Tilapiine fishes of the genera Sarotherodon, Oreochromis and Danakilia. London (UK): British Museum (Natural History).
   Google Scholar
• Villwock W, Scholl A, Krupp F. 1983. Zur Taxonomie, Verbreitung und Speziation des Formenkreises Aphanius dispar (Rüppell, 1828) und Beschreibung von Aphanius sirhani n. sp. (Pisces: Cyprinodontidae). Mitteilungen Aus Dem Hamburgischen Zool Museum Inst. 80:251–277.
   Google Scholar
• Vinciguerra D. 1931. Spedizione del Barone Raimondo Franchetti in Dancalia. Rettili, Batraci e Pesci. Ann Del Museo Civico Di Storia Nat “Giacomo Doria”. 55:96–108.
   Google Scholar
• Wilcox TP, Zwickl DJ, Heath TA, Hillis DM. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol Phylogenet Evol. 25:361–371.
   PubMed Web of Science ®Google Scholar
• Wildekamp RH. 1993. A world of killies. Atlas of the oviparous cyprinodontiform fishes of the world. Vol. 1. The genera Adamas, Adinia, Aphanius, Aphyoplatys and Aphyosemion. Mishawaka (IN): American Killifish Association.
   Google Scholar
• Zardoya R, Doadrio I. 1999. Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids. J Mol Evol. 49:227–237.
   PubMed Web of Science ®Google Scholar