Jordan, D. S. A classification of fishes including families and genera as far as know. Stanford University Publications. Bio. Sci. 3, 79–243. https://doi.org/10.5962/bhl.title.161386 (1923).
Google Scholar
Akihito, et al. Evolutionary aspects of gobioid fishes based on an analysis of mitochondrial cytochrome b genes. Gene 259, 5–15 (2000).
Google Scholar
Wang, H.-Y., Tsai, M.-P., Dean, J. & Lee, S.-C. Molecular phylogeny of gobioid Wshes (Perciformes: Gobioidei) based on mitochondrial 12S rRNA sequences. Mol. Phylogenet. Evol. 20, 390–408. https://doi.org/10.1016/j.ympev.2005.05.004 (2001).
Google Scholar
Nelson, J. S., Grande, T. C. & Wilson, M. V. Fishes of the World (Wiley, 2016).
Google Scholar
Fricke, R., Eschmeyer, W. N. & Van der Laan, R. Eschmeyer’s Catalog of fishes: Genera, Species, references. (http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp) (Accessed 15 June 2022).
Guimarães-Costa, A. et al. Molecular evidence of two new species of Eleotris (Gobiiformes: Eleotridae) in the western Atlantic. Mol. Phylogenet. Evol. 98, 52–56. https://doi.org/10.1016/j.ympev.2016.01.014 (2016).
Google Scholar
Thacker, C. E. & Hardman, M. A. Molecular phylogeny of basal gobioid fishes: Rhyacichthyidae, Odontobutidae, Xenisthmidae, Eleotridae (Teleostei: Perciformes: Gobioidei). Mol. Phylogenet. Evol. 37, 858–887. https://doi.org/10.1016/j.ympev.2005.05.004 (2005).
Google Scholar
Nordlie, F. G. Life-history characteristics of eleotrid fishes of the western hemisphere, and perils of life in a vanishing environment. Rev. Fish Biol. Fisher. 22(1), 189–224. https://doi.org/10.1007/s11160-011-9229-3 (2012).
Google Scholar
Berra, T. M. Freshwater Fish Distribution (Academic Press, 2001).
Graham, J. B. Air-Breathing Fishes: Evolution, Diversity, and Adaptation (Academic Press, 1997).
Google Scholar
Thacker, C. E. Phylogeny of Gobioidea and its placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia 1, 93–104. https://doi.org/10.1643/CI-08-004 (2009).
Google Scholar
Chakrabarty, P., Davis, M. P. & Sparks, J. S. The first record of a trans-oceanic sister-group relationship between obligate vertebrate troglobites. PLoS One 7, e44083. https://doi.org/10.1371/journal.pone.0044083 (2012).
Google Scholar
Agorreta, A. et al. Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies. Mol. Phylogenet. Evol. 69, 619–633. https://doi.org/10.1016/j.ympev.2013.07.017 (2013).
Google Scholar
McCraney, W. T., Thacker, C. E. & Alfaro, M. E. Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria. Mol. Phylogenet. Evol. 151, 106862. https://doi.org/10.1016/j.ympev.2020.106862 (2020).
Google Scholar
Karl, S. A. & Avise, J. C. Balancing selection at allozyme loci in oysters: Implications from nuclear RFLPs. Science 256, 100. https://doi.org/10.1126/science.1348870 (1992).
Google Scholar
Hey, J. & Machado, C. A. The study of structured populations—New hope for a difficult and divided science. Nat. Rev. Genet. 4, 535–543. https://doi.org/10.1038/nrg1112 (2003).
Google Scholar
Castroviejo-Fisher, S., Guayasamin, J. M., Gonzalez-Voyer, A. & Vilà, C. Neotropical diversification seen through glassfrogs. J. Biogeogr. 41, 66–80. https://doi.org/10.1111/jbi.12208 (2014).
Google Scholar
Dornburg, A., Townsend, J. P., Friedman, M. & Near, T. J. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Evol. Biol. 14, 169. https://doi.org/10.1186/s12862-014-0169-0 (2014).
Google Scholar
Hundt, P. J., Iglésias, S. P., Hoey, A. S. & Simons, A. M. A multilocus molecular phylogeny of combtooth blennies (Percomorpha: Blennioidei: Blenniidae): Multiple invasions of intertidal habitats. Mol. Phylogenet. Evol. 70, 47–56. https://doi.org/10.1016/j.ympev.2013.09.001 (2014).
Google Scholar
Olave, M., Avila, L. J., Sites, J. W. & Morando, M. Multilocus phylogeny of the widely distributed South American lizard clade Eulaemus (Liolaemini, Liolaemus). Zool. Scr. 43, 323–337. https://doi.org/10.1111/zsc.12053 (2014).
Google Scholar
Meyer, B. S., Matschiner, M. & Salzburger, W. A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach. Mol. Phylogenet. Evol. 83, 56–71. https://doi.org/10.1016/j.ympev.2014.10.009 (2015).
Google Scholar
Jønsson, K. A. et al. A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides). Mol. Phylogenet. Evol. 94, 87–94. https://doi.org/10.1016/j.ympev.2015.08.020 (2016).
Google Scholar
Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475(7357), 493–496. https://doi.org/10.1038/nature10231 (2011).
Google Scholar
Frantz, R. S. X-efficiency: Theory, Evidence and Applications Vol. 2 (Springer Science & Business Media, 2013).
Bessa-Silva, A. et al. The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex. Mol. Phylogenet. Evol. 145, 106723. https://doi.org/10.1016/j.ympev.2019.106723 (2020).
Google Scholar
Leutenegger, W. Maternal-fetal weight relationships in primates. Folia Primatol. 20(4), 280–293. https://doi.org/10.1159/000155580 (1973).
Google Scholar
Yeh, J. The effect of miniaturized body size on skeletal morphology in frogs. Evolution 56(3), 628–641. https://doi.org/10.1111/j.0014-3820.2002.tb01372.x (2002).
Google Scholar
Daza, J. D. et al. An enigmatic miniaturized and attenuate whole lizard from the Mid-Cretaceous amber of Myanmar. Breviora 563(1), 1–18. https://doi.org/10.3099/MCZ49.1 (2018).
Google Scholar
Hanken, J. & Wake, D. B. Miniaturization of body size: Organismal consequences and evolutionary significance. Annu. Rev. Ecol. Evol. Syst. 24(1), 501–519. https://doi.org/10.1146/annurev.es.24.110193.002441 (1993).
Google Scholar
Britz, R. & Conway, K. W. Osteology of Paedocypris, a miniature and highly developmentally truncated fish (Teleostei: Ostariophysi: Cyprinidae). J. Morphol. 270(4), 389–412. https://doi.org/10.1002/jmor.10698 (2009).
Google Scholar
Britz, R., Conway, K. W. & Ruber, L. Spectacular morphological novelty in a miniature cyprinid fish, Danionella dracula n. sp.. Proc. R. Soc. Lond. 276(1665), 2179–2186. https://doi.org/10.1098/rspb.2009.0141 (2009).
Google Scholar
Weitzman, S. H. & Vari, R. P. Miniaturization in South American freshwater fishes; an overview and discussion. Proc. Biol. Soc. Wash. 101(2), 444–465 (1988).
Toledo-Piza, M., Mattox, G. M. & Britz, R. Priocharax nanus, a new miniature characid from the rio Negro, Amazon basin (Ostariophysi: Characiformes), with an updated list of miniature Neotropical freshwater fishes. Neotrop. Ichthyol. 12(2), 229–246. https://doi.org/10.1590/1982-0224-20130171 (2014).
Google Scholar
Caires, R. A. & Figueiredo, J. L. Review of the genus Microphilypnus Myers, 1927 (Teleostei: Gobioidei: Eleotridae) from the lower Amazon basin, with description of one new species. Zootaxa 3036, 39–57. https://doi.org/10.11646/zootaxa.3036.1.3 (2011).
Google Scholar
Caires, R. A. Microphilypnus tapajosensis, a new species of eleotridid from the Tapajós basin, Brazil (Gobioidei: Eleotrididae). Ichthyol. Explor. Freshw. 23, 155–160 (2013).
Caires, R. A. & Guimarães-Costa, A. Family Eleotridae. In Field Guide to Amazonian Fishes (eds van Sleen, P. & Albert, J.) 388–391 (Princeton University Press, 2017).
Caires, R. A. & Toledo-Piza, M. A New species of miniature fish of the genus Microphilypnus (Gobioidei: Eleotridae) from the upper Rio Negro Basin, Amazonas Brazil. Copeia 106(1), 49–55. https://doi.org/10.1643/CI-17-634 (2018).
Google Scholar
Roberts, T.R. Leptophilypnion, a new genus with two new species of tiny central Amazonian gobioid fishes (Teleostei, Eleotridae). Aqua (2013).
Gould, R. E. & Delevoryas, T. The biology of Glossopteris: Evidence from petrified seed-bearing and pollen-bearing organs. Alcheringa 1(4), 387–399 (1977).
Google Scholar
Rüber, L., Kottelat, M., Tan, H. H., Ng, P. K. & Britz, R. Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the world’s smallest vertebrate. BMC Evol. Biol. 7(1), 1–10. https://doi.org/10.1186/1471-2148-7-38 (2007).
Google Scholar
Britz, R., Conway, K. W. & Rüber, L. Miniatures, morphology and molecules: Paedocypris and its phylogenetic position (Teleostei, Cypriniformes). Zool. J. Linn. Soc. 172(3), 556–615. https://doi.org/10.1111/zoj.12184 (2014).
Google Scholar
Bloom, D. D., Kolmann, M., Foster, K. & Watrous, H. Mode of miniaturisation influences body shape evolution in New World anchovies (Engraulidae). J. Fish Biol. 96(1), 194–201 (2019).
Google Scholar
Thacker, C. E. Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei). Mol. Phylogenet. Evol. 26, 354–368. https://doi.org/10.1016/S1055-7903(02)00361-5 (2003).
Google Scholar
Birdsong, R. S., Murdy, E. O. & Pezold, F. L. A study of the vertebral column and median fin osteology in gobioid fishes with comments on gobioid relationships. Bull. Mar. Sci. 42(2), 174–214 (1988).
Thacker, C. E. Patterns of divergence in fish species separated by the Isthmus of Panama. BMC Evol. Biol. 17(1), 1–14. https://doi.org/10.1186/s12862-017-0957-4 (2017).
Google Scholar
Galván-Quesada, S. et al. Molecular phylogeny and biogeography of the amphidromous fish genus Dormitator Gill 1861 (Teleostei: Eleotridae). PLoS One 11(4), e0153538. https://doi.org/10.1371/journal.pone.0153538 (2016).
Google Scholar
Lessios, H. A. The great American schism: Divergence of marine organisms after therise of the central American isthmus. Annu. Rev. Ecol. Evol. Syst. 2008(39), 63–92. https://doi.org/10.1146/annurev.ecolsys.38.091206.095815 (2008).
Google Scholar
Lovejoy, N. R., Albert, J. S. & Crampton, W. G. Miocene marine incursions and marine/freshwater transitions: Evidence from Neotropical fishes. J. S. Am. Earth Sci. 21, 5–13. https://doi.org/10.1016/j.jsames.2005.07.009 (2006).
Google Scholar
Cooke, G. M., Chao, N. L. & Beheregaray, L. B. Marine incursions, cryptic species and ecological diversification in Amazonia: The biogeographic history of the croaker genus Plagioscion (Sciaenidae). J. Biogeogr. 39, 724–738. https://doi.org/10.1111/j.1365-2699.2011.02635.x (2012).
Google Scholar
Bloom, D. D. & Lovejoy, N. R. On the origins of marine-derived freshwater fishes in South America. J. Biogeogr. 44(9), 1927–1938. https://doi.org/10.1111/jbi.12954 (2017).
Google Scholar
Monsch, K. A. Miocene fish faunas from the northwestern Amazonia basin (Colombia, Peru, Brazil) with evidence of marine incursions. Palaeogeogr. Palaeoclimatol. Palaeoecol. 143, 31–50. https://doi.org/10.1016/S0031-0182(98)00064-9 (1998).
Google Scholar
Hoorn, C. Marine incursions and the influence of Andean tectonics on the Miocene depositional history of northwestern Amazonia: Results of a palynostratigraphic study. Palaeogeogr. Palaeoclimatol. Palaeoecol. 105, 267–309. https://doi.org/10.1016/0031-0182(93)90087-Y (1993).
Google Scholar
Hoorn, C., Guerrero, J., Sarmiento, G. A. & Lorente, M. A. Andean tectonics as a cause for changing drainage patterns in Miocene northern South America. Geology 23, 237–240. https://doi.org/10.1130/0091-7613(1995)023%3C0237:ATAACF%3E2.3.CO;2 (1995).
Google Scholar
Gingras, M. K., Rasanen, M. E., Pemberton, S. G. & Romero, L. P. Ichnology and sedimentology reveal depositional characteristics of bay-margin parasequences in the Miocene Amazonian foreland basin. J. Sediment. Res. 72, 871–883. https://doi.org/10.1306/052002720871 (2002).
Google Scholar
Wesselingh, F. P. et al. Lake Pebas: A palaeoecological reconstruction of a Miocene, long-lived lake complex in western Amazonia. Cainoz. Res. 1, 35–81 (2002).
Bloom, D. D. & Lovejoy, N. R. Molecular phylogenetics reveals a pattern of biome conservatism in New World anchovies (family Engraulidae). J. Evol. Biol. 25(4), 701–715 (2012).
Google Scholar
Ward, A. B. & Azizi, E. Convergent evolution of the head retraction escape response in elongate fishes and amphibians. Zoology 107(3), 205–217. https://doi.org/10.1016/j.zool.2004.04.003 (2004).
Google Scholar
Palumbi, S. R. & Benzie, J. Large mitochondrial DNA differences between morphologically similar penaeid shrimp. Mol. Mar. Biol. Biotechnol. 1, 27–34 (1991).
Google Scholar
Chen, W. J., Bonillo, C. & Lecointre, G. Repeatability of clades as criterion of reliability: A case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa. Mol. Phylogenet. Evol. 26, 262–288. https://doi.org/10.1016/j.gene.2008.07.016 (2003).
Google Scholar
Chen, W. J., Miya, M., Saitoh, K. & Mayden, R. L. Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: The order Cypriniformes (Ostariophysi) as a case study. Gene 423, 125–134. https://doi.org/10.1016/j.gene.2008.07.016 (2008).
Google Scholar
Sanger, F., Nicklen, S. & Coulson, A. R. DNA sequencing with chain-terminating inhibitors. PNAS 74(12), 5463–5467. https://doi.org/10.1073/pnas.74.12.5463 (1977).
Google Scholar
Edgar, R. C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5), 1792–1797. https://doi.org/10.1093/nar/gkh340 (2004).
Google Scholar
Vaidya, G., Lohman, D. J. & Meier, R. SequenceMatrix: Concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 27, 171–180 (2011).
Google Scholar
Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T. & Calcott, B. PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msw260 (2016).
Google Scholar
Heled, J. & Drummond, A. J. Bayesian inference of population size history from multiple loci. BMC Evol. Biol. 8(1), 1–15. https://doi.org/10.1186/1471-2148-8-289 (2008).
Google Scholar
Bouckaert, R. et al. BEAST 2: A software platform for bayesian evolutionary analysis. PLoS Comput. Biol. 10(4), e1003537. https://doi.org/10.1371/journal.pcbi.1003537 (2014).
Google Scholar
Drummond, A. J., Ho, S. Y., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4(5), e88. https://doi.org/10.1371/journal.pbio.0040088 (2006).
Google Scholar
Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67(5), 901. https://doi.org/10.1093/sysbio/syy032 (2018).
Google Scholar
Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214. https://doi.org/10.1186/1471-2148-7-214 (2007).
Google Scholar
Rambaut, A. FigTree, a graphical viewer of phylogenetic trees (Version 1.4.3) (2017).
Betancur-R, R. et al. Phylogenetic classification of bony fishes. BMC Evol. Biol. 17(1), 1–40. https://doi.org/10.1186/s12862-017-0958-3 (2017).
Google Scholar
Jones, G. Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. J. Math. Biol. 74, 447–467 (2017).
Google Scholar
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