Next generation sequencing-aided comprehensive geographic coverage sheds light on the status of rare and extinct populations of Aporia butterflies (Lepidoptera: Pieridae)
1.
Hughes, A. R. & Stachowicz, J. J. Genetic diversity enhances the resistance of a seagrass ecosystem to disturbance. Proc. Natl. Acad. Sci. U.S.A. 101, 8998–9002 (2004).
ADS CAS PubMed PubMed Central Google Scholar
2.
Frankham, R. Genetics and extinction. Biol. Conserv. 126, 131–140 (2005).
Google Scholar
3.
Koizumi, I., Usio, N., Kawai, T., Azuma, N. & Masuda, R. Loss of genetic diversity means loss of geological information: The endangered japanese crayfish exhibits remarkable historical footprints. PLoS ONE 7(3), e33986. https://doi.org/10.1371/journal.pone.0033986 (2012).
ADS CAS Article PubMed PubMed Central Google Scholar
4.
Nazari, V., Schmidt, B. C., Prosser, S. & Hebert, P. D. N. Century-old DNA barcodes reveal phylogenetic placement of the extinct Jamaican Sunset Moth, Urania sloanus Cramer (Lepidoptera: Uraniidae). PLoS ONE 11(10), e0164405. https://doi.org/10.1371/journal.pone.0164405 (2016).
CAS Article PubMed PubMed Central Google Scholar
5.
Nazari, V., Tarmann, G. & Efetov, K. A. Phylogenetic position of the ‘extinct’ Fijian coconut moth, Levuana iridescens (Lepidoptera: Zygaenidae). PLoS ONE 14(12), e0225590. https://doi.org/10.1371/journal.pone.0225590 (2019).
CAS Article PubMed PubMed Central Google Scholar
6.
Kim, Y. S. Illustrated Book of Korean Butterflies in Color (Kyo-Hak Publishing, Seoul, 2002).
Google Scholar
7.
Park, J. S., Cho, Y., Kim, M. J., Nam, S. H. & Kim, I. Description of complete mitochondrial genome of the black-veined white, Aporia crataegi (Lepidoptera: Papilionoidea), and comparison to papilionoid species. J. Asia-Pac. Entomol. 15, 331–341 (2012).
CAS Google Scholar
8.
Park, H. C. et al. DNA barcode analysis for conservation of an endangered species, Aporia crataegi (Lepidoptera, Pieridae) in Korea. J. Seric. Entomol. Sci. 51, 201–206 (2013).
Google Scholar
9.
Della Bruna, C., Gallo, E. & Sbordoni, V. Pieridae, part I (2nd edition). Guide to the Butterflies of the Palearctic Region (ed. Bozano, G. C.) (Omnes Artes, 2013).
10.
Savela, M. Lepidoptera and some other life forms https://www.nic.funet.fi/pub/sci/bio/life/insecta/lepidoptera/ (2018). Accessed 10 November 2019.
11.
Braby, M. F., Vila, R. & Pierce, N. E. Molecular phylogeny and systematics of the Pieridae (Lepidoptera: Papilionoidea): Higher classification and biogeography. Zool. J. Linn. Soc. 147, 239–275 (2006).
Google Scholar
12.
Wahlberg, N., Rota, J., Braby, M. F., Pierce, N. E. & Wheat, C. W. Revised systematics and higher classification of pierid butterflies (Lepidoptera: Pieridae) based on molecular data. Zool. Scr. 43, 641–650 (2014).
Google Scholar
13.
Ding, C. & Zhang, Y. Phylogenetic relationships of Pieridae (Lepidoptera: Papilionoidea) in China based on seven gene fragments. Entomol. Sci. 20, 15–23 (2017).
Google Scholar
14.
Klots, A. B. A generic classification of the Pieridae (Lepidoptera) together with a study of the male genitalia. Entomol. Am. 12, 13–242 (1933).
Google Scholar
15.
Braby, M. F. Provisional checklist of genera of the Pieridae (Lepidoptera: Papilionidae). Zootaxa 832, 1–16 (2005).
Google Scholar
16.
Chou, I. Monograph of Chinese Butterflies, First Volume (Henan Scientific and Technological Publishing House, Zhengzhou, 1999).
Google Scholar
17.
Wu, C. Fauna Sinica, Insecta vol. 52, Lepidoptera, Pieridae (Science Press, Beijing, 2010).
Google Scholar
18.
Ding, C. & Zhang, Y. Phylogenetic relationships of the genera Aporia and Mesapia (Lepidoptera: Pieridae) based on COI and EF1α gene sequences. Acta Entomol. Sin. 59(8), 880–887 (2016).
Google Scholar
19.
Della Bruna, C., Gallo, E., Sbordoni, V. & Bozano, G. C. Addenda to the genus Aporia Hübner, [1819] (Lepidoptera: Pieridae). Nachrichten des Entomologischen Vereins Apollo N. F. 29(4), 205–209 (2009).
Google Scholar
20.
Deodati, T. Filogenesi molecolare, barcoding e stima dei tempi evolutivi in tre gruppi di farfalle diurne (Insecta: Lepidoptera) a distribuzione Sino-Himalayana (PhD thesis) (University of Rome Tor Vergata, 2010).
21.
Allan, P. B. M. Moths and Memories 1st edn. (Watkins & Doncaster, Pudleston, 1948).
Google Scholar
22.
Jugovic, J., Črne, M. & Lužnik, M. Movement, demography and behaviour of a highly mobile species: A case study of the black-veined white, Aporia crataegi (Lepidoptera: Pieridae). Eur. J. Entomol. 114, 113–122 (2017).
Google Scholar
23.
Kim, T. G., Han, Y. G., Kwon, O. & Cho, Y. Changes in Aporia crataegi’s potential habitats in accordance with climate changes in the northeast Asia. J. Ecol. Environ. 38(1), 15–23 (2015).
Google Scholar
24.
van Swaay, C. et al. Aporia crataegi. The IUCN Red List of Threatened Species; https://www.iucnredlist.org (2014). Accessed 10 November 2019.
25.
van Swaay, C. et al. Aporia crataegi. The IUCN Red List of Threatened Species; https://www.iucnredlist.org (2010). Accessed 10 November 2019.
26.
Ivanova, N. V., deWaard, J. R. & Hebert, P. D. N. An inexpensive, automation friendly protocol for recovering high-quality DNA. Mol. Ecol. Notes 6, 998–1002 (2006).
CAS Google Scholar
27.
Prosser, S. W. J., de Waard, J. R., Miller, S. E. & Hebert, P. D. N. DNA barcodes from century-old type specimens using next-generation sequencing. Mol. Ecol. Resour. 16(2), 487–497 (2016).
CAS PubMed Google Scholar
28.
Hajibabaei, M. et al. Critical factors for assembling a high volume of DNA barcodes. Philos. Trans. R. Soc. Lond. B 360, 1959–1967 (2005).
CAS Google Scholar
29.
deWaard, J. R., Ivanova, N. V., Hajibabaei, M. & Hebert, P. D. N. Assembling DNA barcodes: Analytical protocols. Method Mol. Biol. Environ. Genet. 410, 275–293 (2008).
CAS Google Scholar
30.
Librado, P. & Rozas, J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452 (2009).
CAS PubMed PubMed Central Google Scholar
31.
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35(6), 1547–1549 (2018).
CAS PubMed PubMed Central Google Scholar
32.
Bandelt, H. J., Forster, P. & Röhl, A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48 (1999).
CAS PubMed Google Scholar
33.
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
CAS PubMed PubMed Central Google Scholar
34.
Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
CAS PubMed Google Scholar
35.
Stamatakis, A. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21), 2688–2690 (2006).
CAS Google Scholar
36.
Boc, A., Diallo, A. B. & Makarenkov, V. T-REX: A web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res. 40(W1), W573–W579 (2012).
PubMed PubMed Central Google Scholar
37.
Rambaut, A. Figtree v1.4. https://tree.bio.ed.ac.uk/software/figtree (2012). Accessed 23 November 2019.
38.
Kimura, M. Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles. Genet. Res. 11, 247–269 (1968).
CAS PubMed Google Scholar
39.
Ramos-Onsins, S. & Rozas, J. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 19, 2092–2100 (2002).
CAS PubMed Google Scholar
40.
Fu, Y. X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915–925 (1997).
CAS PubMed PubMed Central Google Scholar
41.
Ramirez-Soriano, A., Ramos-Onsins, S. E., Rozas, J., Calafell, F. & Navarro, A. Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination. Genetics 179, 555–567 (2008).
PubMed PubMed Central Google Scholar
42.
Holsinger K. E. Tajima’s D, Fu’s F S, Fay and Wu’s H, and Zeng et al.’s E. in Lecture Notes in Population Genetics (ed. Holsinger, K. E. 2001-2019) 291–296 (University of Connecticut, 2017).
43.
Excoffier, L. & Lischer, H. E. L. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567 (2010).
PubMed PubMed Central Google Scholar
44.
Hudson, R. R. Gene genealogies and the coalescent process. In Oxford Surveys in Evolutionary Biology (eds Futuyma, D. J. & Antonovics, J. D.) 1–44 (Oxford University Press, Oxford, 1990).
Google Scholar
45.
Schneider, S. & Excoffier, L. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: Application to human mitochondrial DNA. Genetics 152, 1079–1089 (1999).
CAS PubMed PubMed Central Google Scholar
46.
Ray, N., Currat, M. & Excoffier, L. Intra-deme molecular diversity in spatially expanding populations. Mol. Biol. Evol. 20, 76–86 (2003).
CAS PubMed Google Scholar
47.
Excoffier, L. Patterns of DNA sequence diversity and genetic structure after a range expansion: Lessons from the infinite-island model. Mol. Ecol. 13, 853–864 (2004).
CAS PubMed Google Scholar
48.
Brower, A. V. Z. Rapid morphological radiation and convergence among races of the butterfly Heliconius erato, inferred from patterns of mitochondrial DNA evolution. Proc. Natl. Acad. Sci. U.S.A. 91, 6491–6495 (1994).
ADS CAS PubMed PubMed Central Google Scholar
49.
Tadokoro, T., Koide, Y. & Hori, K. Description of a new subspecies of Mesapia peloria from central Nepal, and taxonomic notes for other subspecies (Lepidoptera, Pieridae). Lepidoptera Sci. 65(2), 51–59 (2014).
Google Scholar
50.
Schmitt, T. Molecular biogeography of Europe: Pleistocene cycles and postglacial trends. Front. Zool. 4(1), 11 (2007).
PubMed PubMed Central Google Scholar
51.
Dapporto, L. et al. Integrating three comprehensive data sets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies. Mol. Ecol. Resour. 00, 1–14 (2019).
Google Scholar
52.
Ehlers, J., Astakhov, V., Gibbard, P. L., Mangerud, J. & Svendsen, J. I. Late pleistocene glaciations in Europe. In Encyclopedia of Quaternary Science (ed. Elias, S. A.) 1085–1095 (Elsevier, Hoboken, 2006).
Google Scholar
53.
King, R. A. & Ferris, C. Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn. Mol. Ecol. 7, 1151–1161 (1998).
CAS Google Scholar
54.
Wallis, G. P. & Arntzen, J. W. Mitochondrial-DNA variation in the crested newt superspecies: Limited cytoplasmic gene flow among species. Evolution 43, 88–104 (1989).
CAS PubMed Google Scholar
55.
Dapporto, L. Speciation in Mediterranean refugia and post-glacial expansion of Zerynthia polyxena (Lepidoptera, Papilionidae). J. Zool. Syst. Evol. Res. 48(3), 229–237 (2010).
Google Scholar
56.
Galtier, N., Nabholz, B., Glémin, S. & Hurst, G. D. D. Mitochondrial DNA as a marker of molecular diversity: A reappraisal. Mol. Ecol. 18(22), 4541–4550 (2009).
CAS PubMed Google Scholar
57.
Stein, E. D., Martinez, M. C., Stiles, S., Miller, P. E. & Zakharov, E. V. Is DNA barcoding actually cheaper and faster than traditional morphological methods: Results from a survey of freshwater bioassessment efforts in the United States?. PLoS ONE 9(4), e95525. https://doi.org/10.1371/journal.pone.0095525 (2014).
ADS CAS Article PubMed PubMed Central Google Scholar
58.
Sanmartin, I. Dispersal vs. vicariance in the Mediterranean: historical biogeography of the Palearctic Pachydeminae (Coleoptera, Scarabaeoidea). J. Biogeogr. 30, 1883–1897 (2003).
Google Scholar
59.
Krijgsman, W. The Mediterranean: Mare nostrum of earth sciences. Earth Planet. Sci. Lett. 205, 1–12 (2002).
ADS CAS Google Scholar
60.
Steininger, F. F. & Rogl, F. Paleogeography and palinspastic reconstruction of the Neogene of the Mediterranean and Paratethys. In The Geological Evolution of the Eastern Mediterranean (eds Dixon, J. E. & Robertson, A. H. F.) 659–668 (Geological Society Special Publication. Blackwell Scientific Publications, Hoboken, 1996).
Google Scholar
61.
De Jong, H. In search of historical biogeographic patterns in the western Mediterranean terrestrial fauna. Biol. J. Linnean Soc. 65, 99–164 (1998).
Google Scholar
62.
Nazari, V., Ten Hagen, W. & Bozano, G. C. Molecular systematics and phylogeny of the ‘Marbled Whites’ (Lepidoptera: Nymphalidae, Satyrinae, Melanargia Meigen). Syst. Entomol. 35, 132–147 (2010).
Google Scholar
63.
Todisco, V. et al. Molecular phylogeny of the Palaearctic butterfly genus Pseudophilotes (Lepidoptera: Lycaenidae) with focus on the Sardinian endemic P. barbagiae. BMC Zool. 3, 4 (2018).
Google Scholar
64.
Dinca, V., Dapporto, L. & Vila, R. A combined genetic-morphometric analysis unravels the complex biogeographical history of Polyommatus icarus and Polyommatus celina common blue butterflies. Mol. Ecol. 20, 3921–3935 (2011).
CAS PubMed Google Scholar
65.
Sañudo-Restrepo, C. P., Dinca, V., Talavera, G. & Vila, R. Biogeography and systematics of Aricia butterflies (Lepidoptera, Lycaenidae). Mol. Phylogenet. Evol. 66, 369–379 (2013).
PubMed Google Scholar More