References
- Anderson E. 1949. Introgressive hybridization. New York, USA: Wiley & Sons; p. 1–109.
- Avise JC. 1994. Molecular markers, natural hislory & evolution. New York, USA: Chapman & Hall; p. 1–511.
- Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC. 1987. Intraspecific phylogeography: The mitochondrial bridge between population genetics and systematics. Annual Review of Ecology, Evolution, and Systematics. 18:489–522. doi:https://doi.org/10.1146/annurev.es.18.110187.002421
- Barber BR, Xu J, Pérez-Losada M, Jara CG, Crandall KA. 2012. Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis. PLoS One. 7(6):e37105. doi:https://doi.org/10.1371/journal.pone.0037105
- Bensasson D, Zhang D-X, Hartl DL, Hewitt GM. 2001. Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends in Ecology & Evolution. 16:314–321. doi:https://doi.org/10.1016/S0169-5347(01)02151-6
- Blaxter ML. 2004. The promise of a DNA taxonomy. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 359:669–679. doi:https://doi.org/10.1098/rstb.2003.1447
- Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, et al. 2019. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLOS Computational Biology 15:e1006650. doi:https://doi.org/10.1371/journal.pcbi.1006650
- Cannicci S, Schubart CD, Innocenti G, Dahdouh-Guebas F, Shahdadi A, Fratini S. 2017. A new species of the genus Parasesarma De Man 1895 from East African mangroves and evidence for mitochondrial introgression in sesarmid crabs. Zoologischer Anzeiger. 269:89–99. doi:https://doi.org/10.1016/j.jcz.2017.08.002
- Chan KMA, Levin SA. 2005. Leaky prezygotic isolation and porous genomes: rapid introgression of maternally inherited DNA. Evolution. 59:720–729. doi:https://doi.org/10.1111/j.0014-3820.2005.tb01748.x
- Clarke B, Johnson MS, Murray J. 1996. Clines in the genetic distance between two species of island land snails: how ‘molecular leakage’ mislead us about speciation. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 351:773–784. doi:https://doi.org/10.1098/rstb.1996.0072
- Darling JA. 2011. Interspecific hybridization and mitochondrial introgression in invasive Carcinus shore crabs. PLoS One. 6(3):e17828: 1–10. doi:https://doi.org/10.1371/journal.pone.0017828
- Davie PJF. 1994. Variations in diversity of mangrove crabs in tropical Australia. Memoirs of the Queensland Museum. 36:55–58.
- Felsenstein J. 1988. Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics. 22:521–565. doi:https://doi.org/10.1146/annurev.ge.22.120188.002513
- Funk DJ, Omland KE. 2003. Species-level paraphyly and polyphyly: frequency, causes and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics. 34:397–423. doi:https://doi.org/10.1146/annurev.ecolsys.34.011802.132421
- Grant PR, Grant BR, Petren K. 2005. Hybridization in the recent past. The American Naturalist. 166(1):56–67. doi:https://doi.org/10.1086/430331
- Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA. 2007. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics. 23:167–172. doi:https://doi.org/10.1016/j.tig.2007.02.001
- Hall TA. 1999. Bioedit: a user–friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series 41:95–98.
- Harrison R. 2014. Hybridization, introgression, and the nature of species boundaries. Journal of Heredity. 105:795–809. doi:https://doi.org/10.1093/jhered/esu033
- Hebert PDN, Cywinska A, Ball SL, de Waard JR. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences 270:313–321. doi:https://doi.org/10.1098/rspb.2002.2218
- Hubbs CL. 1955. Hybridization between fish species in nature. Systematic Zoology. 4:1–20. doi:https://doi.org/10.2307/2411933
- Joly S. 2012. JML: testing hybridization from species trees. Molecular Ecology Resources. 12(1):179–184. doi:https://doi.org/10.1111/j.1755-0998.2011.03065.x
- Joly S, McLenachan PA, Lockhart PJ. 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am. Nat. 174:E54–E70. doi:https://doi.org/10.1086/600082
- Lee SY. 1998. Ecological role of grapsid crabs in mangrove ecosystems: A review. Marine and Freshwater Research. 49:335–43. doi:https://doi.org/10.1071/MF97179
- Lee SY. 2015. Ecology of Brachyura. In: Castro P, Davie PJF, Guinot D, Schram F, von Vaupel Klein C, editor. Treatise on zoology - anatomy, taxonomy, biology - The crustacea, complementary to the volumes translated from the French of the Traité de Zoologie. Leiden: Brill. 9(C) (I); p. 469–542.
- Leigh JW, Bryant D. 2015. PopART: Full-feature software for haplotype network construction. Methods in Ecology and Evolution. 6:1110–1116. doi:https://doi.org/10.1111/2041-210X.12410
- Librado P, Rozas J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics (oxford, England). 25:1451–1452. doi:https://doi.org/10.1093/bioinformatics/btp187
- Lyubetsky V, Piel WH, Quandt D. 2014. Current advances in molecular phylogenetics. BioMed Research International. 2014:1–2. doi:https://doi.org/10.1155/2014/596746
- Manning RB, Holthuis LB. 1981. West African brachyuran crabs (Crustacea: Decapoda). Smithsonian Contributions to Zoology. 306:1–379. doi:https://doi.org/10.5479/si.00810282.306
- Monod T. 1956. Hippidea et Brachyura ouest–africains. Mémoires de l'Institut Français d'Afrique Noire. 45:1–674.
- Moritz C, Cicero C. 2004. DNA barcoding: promise and pitfalls. PLoS Biology. 2:e312. doi:https://doi.org/10.1371/journal.pbio.0020354
- Ng PKL, Guinot D, Davie PJF. 2008. Systema brachyurorum: part I. An annotated checklist of extant brachyuran crabs of the world. Raffles Bulletin of Zoology. 17:1–286.
- Ottenburghs J. 2020. Ghost introgression: spooky gene flow in the distant past. BioEssays. 42(6):e2000012. doi:https://doi.org/10.1002/bies.202000012
- Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology. 53:793–808. doi:https://doi.org/10.1080/10635150490522304
- Rieseberg LH, Sinervo B, Linder CR, Ungerer MC, Arias DM. 1996. Role of gene interactions in hybrid speciation: evidence from ancient and experimental hybrids. Science. 272:741–745. doi:https://doi.org/10.1126/science.272.5262.741
- Rodriguez FJ, Oliver JL, Marin A, Medina JR. 1990. The general stochastic model of nucleotide substitution. Journal of Theoretical Biology. 142:485–501. doi:https://doi.org/10.1016/S0022-5193(05)80104-3
- Rodríguez-Pena E, Verísimo P, Fernández L, González-Tizón A, Bárcena C, Martínez-Lage A. 2020. High incidence of heteroplasmy in the mtDNA of a natural population of the spider crab Maja brachydactyla. PLoS One. 15(3):e0230243. doi:https://doi.org/10.1371/journal.pone.0230243
- Rogers AR, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution. 19:552–569. doi:https://doi.org/10.1093/oxfordjournals.molbev.a040727
- Shaw KL. 2002. Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: what mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. Proceedings of the National Academy of Sciences of the USA. 99:16122–16127. doi:https://doi.org/10.1073/pnas.242585899
- Schubart CD. 2009. Mitochondrial DNA and decapod phylogenies: the importance of pseudogenes and primer optimization. In: Martin J.W., Crandall K.A., Felder D.L., editor. Decapod Crustacean phylogenetics. Crustac. Iss. 18. London: RCP Press; p. 47–65.
- Schubart CD, Cuesta JA, Diesel R, Felder DL. 2000. Molecular phylogeny, taxonomy, and evolution of non-marine lineages within the American grapsoid crabs (Crustacea: Brachyura). Molecular Phylogenetics and Evolution. 15:179–190. doi:https://doi.org/10.1006/mpev.1999.0754
- Schubart CD, Diesel R, Hedges S. 1998. Rapid evolution to terrestrial life in Jamaican crabs. Nature. 393:363–365. doi:https://doi.org/10.1038/30724
- Schubart CD, Huber MGJ. 2006. Genetic comparison of German populations of the stone crayfish, Austropotamobius torrentium (Crustacea: Astacidae). Bulletin Français de la Pêche et de la Pisciculture. 380–381:1019–1028. doi:https://doi.org/10.1051/kmae:2006008
- Schubart CD, Santl T, Koller P. 2008. Mitochondrial patterns of intra- and interspecific differentiation among endemic freshwater crabs of ancient lakes in sulawesi. Contributions to Zoology. 77:83–90. doi:https://doi.org/10.1163/18759866-07702004
- Schubart CD, Weil T, Stenderup JT, Crandall KA, Santl T. 2010. Ongoing phenotypic and genotypic diversification in adaptively radiated freshwater crabs from Jamaica. In: M. Glaubrecht, editor. Evolution in action - adaptive radiations and the origins of biodiversity. Heidelberg: Springer-Verlag Berlin; p. 323–349.
- Shahdadi A, Davie PJF, Schubart CD. 2019a. A new species of Parasesarma (Decapoda: Brachyura: Sesarmidae) from northern Australian mangroves and its distinction from morphologically similar species. Zoologischer Anzeiger. 279:116–125. doi:https://doi.org/10.1016/j.jcz.2019.01.005
- Shahdadi A, Fratini S, Schubart CD. 2020. Taxonomic reassessment of Parasesarma De Man, 1895 (Crustacea: Brachyura: Decapoda: Sesarmidae) based on genetic and morphological comparisons, with description of a new genus. Zoological Journal of the Linnean Society 190(4):1123–1158. doi:https://doi.org/10.1093/zoolinnean/zlaa025
- Shahdadi A, Mvogo Ndongo PA, Suess T, Schubart CD. 2019b. Reappraisal and redescription of the three species of the recently defined genus Guinearma Shahdadi & schubart, 2017, with a key to the West African Sesarmidae (Decapoda, Brachyura). Crustaceana. 92:307–334. doi:https://doi.org/10.1163/15685403-00003863
- Shahdadi A, Schubart CD. 2017. Taxonomic review of Perisesarma (Decapoda: Brachyura: Sesarmidae) and closely related genera based on morphology and molecular phylogenetics: new classification, two new genera and the questionable phylogenetic value of the epibranchial tooth. Zoological Journal of the Linnean Society. 182:517–548. doi:https://doi.org/10.1093/zoolinnean/zlx032
- Silvestro D, Michalak I. 2012. RAxML GUI: a graphical front-end for RAML. Organisms Diversity & Evolution. 12:335–337. doi:https://doi.org/10.1007/s13127-011-0056-0
- Simon C, Frati F, Beckenbach A, Crespi B, Liu H, Flook P. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Annals of the Entomological Society of America. 87(6):651–701. doi:https://doi.org/10.1093/aesa/87.6.651
- Smith GR. 1992. Introgression in fishes: significance for paleontology, cladistics, and evolutionary rates. Systematic Biology. 41:41–57. doi:https://doi.org/10.1093/sysbio/41.1.41
- Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony method. Molecular Biology and Evolution. 28:2731–2739. doi:https://doi.org/10.1093/molbev/msr121
- Tan CGS, Ng PKL. 1994. An annotated checklist of mangrove brachyuran crabs from Malaysia and Singapore. Hydrobiologia. 285:75–84. doi:https://doi.org/10.1007/BF00005655
- 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. doi:https://doi.org/10.1093/genetics/132.2.619
- Toews DPL, Brelsford A. 2012. The biogeography of mitochondrial and nuclear discordance in animals. Molecular Ecology. 21:3907–3930. doi:https://doi.org/10.1111/j.1365-294X.2012.05664.x
- Thompson JD, Higgins DG, Gibson TJ. 1994. Clustal W: improving the sensitivity of progressive multiples sequence alignments through sequence weighting, position–specific gap penalties and weight matrix choice. Nucleic Acids Research. 22:4673–4680. doi:https://doi.org/10.1093/nar/22.22.4673
- Tsang LM, Ma KY, Ahyong ST, Chan TY, Chu KH. 2008. Phylogeny of Decapoda using two nuclear protein-coding genes: origin and evolution of the Reptantia. Molecular Phylogenetics and Evolution. 48:359–368. doi:https://doi.org/10.1016/j.ympev.2008.04.009
- Tsang LM, Schubart CD, Ahyong ST, Lai JC, Au EY, Chan TY, Ng PK, Chu KH. 2014. Evolutionary history of true crabs (Crustacea: Decapoda: Brachyura) and the origin of freshwater crabs. Molecular Biology and Evolution. 31:1173–1187. doi:https://doi.org/10.1093/molbev/msu068
- Wirtz P. 1999. Mother species–father species: unidirectional hybridization in animals with female choice. Animal Behaviour. 58:1–12. doi:https://doi.org/10.1006/anbe.1999.1144