21
Views
0
CrossRef citations to date
0
Altmetric
Research Article

DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia

, ORCID Icon, ORCID Icon, &
Received 06 Mar 2023, Accepted 14 Mar 2024, Published online: 20 Jun 2024

References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2.
  • Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16(1):37–48. doi: 10.1093/oxfordjournals.molbev.a026036.
  • Bensasson D, Zhang D, Hartl DL, Hewitt GM. 2001. Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol. 16(6):314–321. PMID: 11369110. doi: 10.1016/s0169-5347(01)02151-6.
  • Boero F, Bernardi G. 2014. Phenotypic vs genotypic approaches to biodiversity, from conflict to alliance. Mar Genomics. 17:63–64. Epub 2014 Apr 2. PMID: 24703835. doi: 10.1016/j.margen.2014.03.005.
  • Bohonak AJ. 2002. IBD (Isolation By Distance): a program for analyses of isolation by distance. J Hered. 93(2):153–154. doi: 10.1093/jhered/93.2.153.
  • Cordaux R, Michel-Salzat A, Bouchon D. 2001. Wolbachia infection in crustaceans: novel hosts and potential routes for horizontal transmission. J Evol Biol. 14(2):237–243. doi: 10.1046/j.1420-9101.2001.00279.x.
  • Cordaux R, Pichon S, Hatira HB, Doublet V, Grève P, Marcadé I, Braquart-Varnier C, Souty-Grosset C, Charfi-Cheikhrouha F, Bouchon D. 2012. Widespread Wolbachia infection in terrestrial isopods and other crustaceans. Zookeys. 176(176):123–131. doi: 10.3897/zookeys.176.2284.
  • Correa CC, Ballard JWO. 2016. Wolbachia associations with insects: winning or losing against a master manipulator. Front Ecol Evol. 3:153. doi: 10.3389/fevo.2015.00153.
  • Cristescu ME. 2014. From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends Ecol Evol. 29(10):566–571. doi: 10.1016/j.tree.2014.08.001.
  • Dimitriou AC, Taiti S, Sfenthourakis S. 2019. Genetic evidence against monophyly of Oniscidea implies a need to revise scenarios for the origin of terrestrial isopods. Sci Rep. 9(1):18508. doi: 10.1038/s41598-019-55071-4.
  • Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 29(8):1969–1973. Epub 2012 Feb 25. PMID: 22367748; PMCID: PMC3408070. doi: 10.1093/molbev/mss075.
  • Eberl R, Mateos M, Grosberg RK, Santamaria CA, Hurtado LA. 2013. Phylogeography of the supralittoral isopod Ligia occidentalis around the Point Conception marine biogeographical boundary. J Biogeogr. 40(12):2361–2372. doi: 10.1111/jbi.12168.
  • Excoffier L, Lischer HE. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 10(3):564–567. doi: 10.1111/j.1755-0998.2010.02847.x.
  • Farjallah S, Amor N, Garippa G, Montero FE, Víllora-Montero M, Mohamed OB, Merella P. 2023. Genetic variation of Sparicotyle chrysophrii (Monogenea: Microcotylidae) from the gilthead sea bream Sparus aurata (Teleostei: Sparidae) in the Mediterranean Sea. Parasitol Res. 122(1):157–165. PMID: 36418649. doi: 10.1007/s00436-022-07709-y.
  • 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(5):294–299.
  • Grummer JA, Bryson RW, Jr, Reeder TW. 2014. Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae). Syst Biol. 63(2):119–133. doi: 10.1093/sysbio/syt069.
  • Harigai W, Saito A, Zemmoto C, Karasawa S, Yokoi T, Nagano AJ, Suzuki H, Yamamoto M. 2023. History of the terrestrial isopod genus Ligidium in Japan based on phylogeographic analysis. BMC Ecol Evo. 23(1):38. doi: 10.1186/s12862-023-02144-8.
  • Hebert PDN, Cywinska A, Ball SL, De Waard JR. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences. 270. p. 313–321.
  • Hsü KJ, Ryan WBF, Cita MB. 1973. Late Miocene desiccation of the Mediterranean. Nature. 242(5395):240–244. doi: 10.1038/242240a0.
  • Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17(8):754–755. doi: 10.1093/bioinformatics/17.8.754.
  • Hurst GDD, Jiggins FM. 2005. Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proc R Soc B. 272(1572):1525–1534. doi: 10.1098/rspb.2005.3056.
  • Hurtado LA, Lee EJ, Mateos M, Taiti S. 2014. Global diversification at the harsh sea-land interface: mitochondrial phylogeny of the supralittoral isopod genus Tylos (Tylidae, Oniscidea). PLoS One. 9(4):e94081. doi: 10.1371/journal.pone.0094081.
  • Hurtado LA, Mateos M, Santamaria CA. 2010. Phylogeography of supralittoral rocky intertidal Ligia isopods in the Pacific region from Central California to Central Mexico. PLoS One. 5(7):e11633. [PMC free article],
  • Jung J, Eo HS, Rho RS, Kim W. 2008. Two genetic lineages of sea slaters, Ligia (Crustacea: Isopoda) in South Korea: a population genetic approach. Mol Cells. 25(4):523–530. doi: 10.1016/S1016-8478(23)17613-8.
  • Kelly LJ, Hollingsworth PM, Coppins BJ, Ellis CJ, Harrold P, Tosh J, Yahr R. 2011. DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. New Phytol. 191(1):288–300. doi: 10.1111/j.1469-8137.2011.03677.x.
  • Klossa-Kilia E, Kilias G, Tryfonopoulos G, Koukou K, Sfenthourakis S, Parmakelis A. 2006. Molecular phylogeny of the Greek populations of the genus Ligidium (Isopoda, Oniscidea) using three mtDNA gene segments. Zool Scr. 35(5):459–472. doi: 10.1111/j.1463-6409.2006.00243.x.
  • Krijgsman W, Langereis CG, Zachariasse WJ, Boccaletti M, Moratti G, Gelati R, Iaccarino S, Papani G, Villa G. 1999. Late Neogene evolution of the Taza-Guercif Basin (Rifi an Corridor, Morocco) and implications for the Messinian salinity crisis. Mar Geol. 153(1–4):147–160. doi: 10.1016/S0025-3227(98)00084-X.
  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 35(6):1547–1549. doi: 10.1093/molbev/msy096.
  • Laifi N, Ben Souissi E, Gabsi F, Medini-Bouazizi L. 2020. Redescription et répartition géographique de Ligia italica (crustacé, isopode) en Tunisie. Bull Inst Natn Scien Tech Mer de Salammbô. 47:97.
  • Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. 2016. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol. 34(3):772–773. doi: 10.1093/molbev/msw260.
  • Legendre P, Fortin M-J. 2010. Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Mol Ecol Resour. 10(5):831–844. doi: 10.1111/j.1755-0998.2010.02866.x.
  • Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25(11):1451–1452. doi: 10.1093/bioinformatics/btp187.
  • Lumivero. 2023. XLSTAT statistical and data analysis solution. https://www.xlstat.com/en.
  • Manzi V, Gennari R, Hilgen F, Krijgsman W, Lugli S, Roveri M, Sierro FJ. 2013. Age refinement of the Messinian salinity crisis onset in the Mediterranean. Terra Nova. 25(4):315–322. doi: 10.1111/ter.12038.
  • Markow TA, Pfeiler E. 2010. Mitochondrial DNA evidence for deep genetic divergences in allopatric populations of the rocky intertidal isopod Ligia occidentalis from the eastern Pacific. Mol Phylogenet Evol. 56(1):468–473. doi: 10.1016/j.ympev.2009.12.002.
  • Miller MP. 2005. Alleles In Space (AIS): computer Software for the Joint Analysis of Interindividual Spatial and Genetic Information. J Hered. 96(6):722–724. doi: 10.1093/jhered/esi119.
  • Ogilvie HA, Bouckaert RR, Drummond AJ. 2017. StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates. Mol Biol Evol. 34(8):2101–2114. PMID: 28431121; PMCID: PMC5850801. doi: 10.1093/molbev/msx126.
  • Okonechnikov K, Golosova O, Fursov M, the UGENE team. 2012. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 28(8):1166–1167. doi: 10.1093/bioinformatics/bts091.
  • Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol. 55(4):595–609. doi: 10.1080/10635150600852011.
  • Puillandre N, Brouillet S, Achaz G. 2020. ASAP: assemble species by automatic partitioning. Mol Ecol Resour. 21(2):609–620. PMID: 33058550. doi: 10.1111/1755-0998.13281.
  • Puillandre N, Lambert A, Brouillet S, Achaz G. 2012. ABGD, automatic barcode gap discovery for primary species delimitation. Mol Ecol. 21(8):1864–1877. doi: 10.1111/j.1365-294X.2011.05239.x.
  • Rambaut A, Drummond A. 2007. Tracer 1.5. 0. Edinburgh, UK: University of Edinburgh. Available at: http://beast.bio.ed.ac.uk/Tracer.
  • Raupach MJ, Rulik B, Spelda J. 2022. Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). Zookeys. 1082:103–125. doi: 10.3897/zookeys.1082.69851.
  • Ray N, Currat M, Excoffier L. 2003. Intra-deme molecular diversity in spatially expanding populations. Mol Biol Evol. 20(1):76–86. doi: 10.1093/molbev/msg009.
  • Rousset F. 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics. 145(4):1219–1228. PMID: 9093870; PMCID: PMC1207888. doi: 10.1093/genetics/145.4.1219.
  • Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 34(12):3299–3302. doi: 10.1093/molbev/msx248.
  • Santamaria CA, Mateos M, DeWitt TJ, Hurtado LA. 2016. Constrained body shape among highly genetically divergent allopatric lineages of the supralittoral isopod Ligia occidentalis (Oniscidea). Ecol Evol. 6(5):1537–1554. doi: 10.1002/ece3.1984.
  • Santamaria CA, Mateos M, Hurtado LA. 2014. Diversification at the narrow sea-land interface in the Caribbean: phylogeography of endemic supralittoral Ligia isopods. Front Ecol Evol. 2(2):42. doi: 10.3389/fevo.2014.00042.
  • Santamaria CA, Mateos M, Taiti S, De Witt TJ, Hurtado LA. 2013. A complex evolutionary history in a remote archipelago: phylogeography and morphometrics of the Hawaiian endemic Ligia Isopods. PLoS One. 8(12):e85199. doi: 10.1371/journal.pone.0085199.
  • Schizas NV. 2012. Misconceptions regarding nuclear mitochondrial pseudogenes (numts) may obscure detection of mitochondrial novelties. Aquat Biol. 17(1):91–96. doi: 10.3354/ab00478.
  • Stamatakis A. 2006. Raxml-vi-hpc: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21):2688–2690. doi: 10.1093/bioinformatics/btl446.
  • Stöck M, Grifoni G, Armor N, Scheidt U, Sicilia A, Novarini N. 2016. On the origin of the recent herpetofauna of Sicily: comparative phylogeography using homologous mitochondrial and nuclear genes. Zool Anz J Comparat Zool. 261:70–81. volumedoi: 10.1016/j.jcz.2015.10.005.
  • Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. 2018. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4(1):vey016. doi: 10.1093/ve/vey016.
  • Taiti S, Arnedo MA, Lew SE, Roderick GK. 2003. Evolution of terrestriality in Hawaiian species of the genus Ligia (Isopoda, Oniscidea) Crustaceana Monographs. The Biology of Terrestrial Isopods 2:85–102. [Google Scholar].
  • Vandel A. 1960. Isopodes terrestres (première partie). In: Lechevalier P, editor. Faune de France. Paris; p. 1–416.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.