Publication Cover
Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 31, 2020 - Issue 3
210
Views
3
CrossRef citations to date
0
Altmetric
Research Articles

Strong genetic differentiation among populations of Cheirotonus gestroi (Coleoptera: Euchiridae) in its native area sheds lights on species conservation

, , , , , & show all
Pages 108-119 | Received 14 Jan 2020, Accepted 08 Mar 2020, Published online: 23 Mar 2020

References

  • Allendorf FW, England PR, Luikart G, Ritchie PA, Ryman N. 2008. Genetic effects of harvest on wild animal populations. Trends Ecol Evol. 23:327–337.
  • Allendorf FW, Hohenlohe PA, Luikart G. 2010. Genomics and the future of conservation genetics. Nat Rev Genet. 11:697–709.
  • Avise JC. 1994. Molecular markers, natural history and evolution. [New York]: Chapman and Hall.
  • Baele G, Li WLS, Drummond AJ, Suchard MA, Lemey P. 2012. Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol Biol Evol. 30:239–243.
  • Beerli P, Felsenstein J. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci USA. 98:4563–4568.
  • 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 Comput Biol. 15:e1006650.,
  • Bowen BW. 2016. The three domains of conservation genetics: case histories from Hawaiian waters. JHERED. 107:309–317.
  • Brown WM, George M, Wilson AC. 1979. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA. 76:1967–1971.
  • Campbell EO, Gage EV, Gage RV, Sperling FA. 2019. Single nucleotide polymorphism-based species phylogeny of greater fritillary butterflies (Lepidoptera: Nymphalidae: Speyeria) demonstrates widespread mitonuclear discordance. Syst Entomol. 45:269–280.
  • Chen J, Yang Y, Sun H. 2011. Advances in the studies of responses of alpine plants to global warming. Chin J Appl Environ Biol. 17:435–446.
  • Cheng L, Connor TR, Sirén J, Aanensen DM, Corander J. 2013. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol Biol Evol. 30:1224–1228.
  • Chikhi L, Sousa VC, Luisi P, Goossens B, Beaumont MA. 2010. The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics. 186:983–995.
  • Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Mol Ecol. 9:1657–1659.
  • Cohen KM, Finney SC, Gibbard PL, Fan JX. 2013. The ICS international chronostratigraphic chart. Episodes. 36:199–204.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods . 9:772–772.
  • Diringer B, Pretell K, Avellan R, Chanta C, Cedeño V, Gentile G. 2019. Genetic structure, phylogeography, and demography of Anadara tuberculosa (Bivalvia) from East Pacific as revealed by mtDNA: implications to conservation. Ecol Evol. 9:4392–4402.
  • Dixo M, Metzger JP, Morgante JS, Zamudio KR. 2009. Habitat fragmentation reduces genetic diversity and connectivity among toad populations in the Brazilian Atlantic Coastal Forest. Biol Conserv. 142:1560–1569.
  • Dray S, Dufour AB. 2007. The ade4 package: implementing the duality diagram for ecologists. J Stat Softw. 22:1–20.
  • Duan X, Wang K, Su S, Tian R, Li Y, Chen M. 2017. De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.)(Hemiptera: Aphididae). PLoS One. 12:e0172513.
  • 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. 10:564–567.
  • Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit 1 from diverse metazoan invertebrates. Mol Mar Biol Biotechnol. 3:294–299.
  • Frankham R. 2003. Genetics and conservation biology. C R Biol. 326:22–29.
  • Froufe E, Sobral C, Teixeira A, Sousa R, Varandas S, C. Aldridge D, Lopes-Lima M. 2014. Genetic diversity of the pan-European freshwater mussel Anodonta anatina (Bivalvia: Unionoida) based on CO1: new phylogenetic insights and implications for conservation. Aquatic Conserv: Mar Freshw Ecosyst. 24:561–574.
  • Galtier N, Enard D, Radondy Y, Bazin E, Belkhir K. 2006. Mutation hot spots in mammalian mitochondrial DNA. Genome Res. 16:215–222.
  • Govindaraj M, Vetriventhan M, Srinivasan M. 2015. Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int. 2015:431487.
  • Gradish AE, Keyghobadi N, Sperling FAH, Otis GW. 2019. Population genetic structure and assessment of allochronic divergence in the Macoun’s Arctic (Oeneis macounii) butterfly. Can J Zool. 97:121–130.
  • Hadjistylli M, Roderick GK, Brown JK. 2016. Global population structure of a worldwide pest and virus vector: genetic diversity and population history of the Bemisia tabaci sibling species group. PloS One. 11:e0165105.
  • Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, in: Nucleic Acids Symposium Series. [London]: Information Retrieval, p. 95–98.
  • 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. 270:S96–S99.
  • Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature. 405:907–913.
  • Huang JP. 2019. Holocene population decline and conservation implication for the Western Hercules Beetle, Dynastes grantii (Coleoptera, Scarabaeidae). J Hered. 110:629–637.
  • Johansson T. 2007. Biomass production and allometric above-and below-ground relations for young birch stands planted at four spacings on abandoned farmland. Forestry. 80:41–52.
  • Kang AR, Kim KG, Park JW, Kim I. 2012. Genetic diversity of the dung beetle, Copris tripartitus (Coleoptera: Scarabaeidae), that is endangered in Korea: genetic diversity of Copris tripartitus. Entomol Res. 42:247–261.
  • Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 9:286–298.
  • Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111–120.
  • Lefébure T, Douady CJ, Gouy M, Gibert J. 2006. Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Mol Phylogenet Evol. 40:435–447.
  • Leigh JW, Bryant D. 2015. popart: full-feature software for haplotype network construction. Methods Ecol Evol. 6:1110–1116.
  • Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
  • Loarie SR, Duffy PB, Hamilton H, Asner GP, Field CB, Ackerly DD. 2009. The velocity of climate change. Nature. 462:1052–1055.
  • Luikart G, Ryman N, Tallmon DA, Schwartz MK, Allendorf FW. 2010. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conserv Genet. 11:355–373.
  • Mairal M, Sanmartín I, Herrero A, Pokorny L, Vargas P, Aldasoro JJ, Alarcón M. 2017. Geographic barriers and Pleistocene climate change shaped patterns of genetic variation in the Eastern Afromontane biodiversity hotspot. Sci Rep. 7:45749.
  • Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res. 27:209–220.
  • Mekonnen A, Rueness EK, Stenseth NC, Fashing PJ, Bekele A, Hernandez-Aguilar RA, Missbach R, Haus T, Zinner D, Roos C. 2018. Population genetic structure and evolutionary history of Bale monkeys (Chlorocebus djamdjamensis) in the southern Ethiopian Highlands. BMC Evol Biol. 18:106.
  • Meng L, Chen G, Li Z, Yang Y, Wang Z, Wang L. 2015. Refugial isolation and range expansions drive the genetic structure of Oxyria sinensis (Polygonaceae) in the Himalaya-Hengduan Mountains. Sci Rep. 5:10396.
  • Meusnier I, Singer GA, Landry JF, Hickey DA, Hebert PD, Hajibabaei M. 2008. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics. 9:214.
  • Minh BQ, Nguyen MAT, von Haeseler A. 2013. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 30:1188–1195.
  • Miranda EA, Ferreira KM, Carvalho AT, Martins CF, Fernandes CR, Del Lama MA. 2017. Pleistocene climate changes shaped the population structure of Partamona seridoensis (Apidae, Meliponini), an endemic stingless bee from the Neotropical dry forest. PLoS One. 12:e0175725.
  • Monaghan MT, Balke M, Gregory TR, Vogler AP. 2005. DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Phil Trans R Soc B. 360:1925–1933.
  • Moritz C. 1994. Defining ‘evolutionarily significant units’ for conservation. Trends Ecol Evol. 9:373–375.
  • Muramoto M. 2008. A new species of the genus Cheirotonus Hope, 1840 from Tibet, with a list of the genus Cheirotonus (Coleoptera, Scarabaeidae, Euchirinae). Kogane. 9:85–94.
  • Myers N, Mittermeier RA, Mittermeier CG, Da Fonseca GA, Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature. 403:853–858.
  • Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32:268–274.
  • Nogués-Bravo D, Araújo MB, Errea MP, Martinez-Rica JP. 2007. Exposure of global mountain systems to climate warming during the 21st Century. Glob Environ Change. 17:420–428.
  • Nunziata SO, Weisrock DW. 2018. Estimation of contemporary effective population size and population declines using RAD sequence data. Heredity. 120:196–207.
  • Papadopoulou A, Anastasiou I, Vogler AP. 2010. Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration. Mol Biol Evol. 27:1659–1672.
  • Pauli H, Gottfried M, Grabherr G. 1996. Effects of climate change on mountain ecosystems–upward shifting of alpine plants. World Resour Rev. 8.
  • Petit RJ, Aguinagalde I, de Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M. 2003. Glacial refugia: hotspots but not melting pots of genetic diversity. Science. 300:1563–1565.
  • Phalen DN, Hall J, Ganesh G, Hartigan A, Smith C, De Jong C, Field H, Rose K. 2017. Genetic diversity and phylogeny of the Christmas Island flying fox (Pteropus melanotus natalis). J Mammal. 98:428–437.
  • Phillips SJ, Anderson RP, Dudík M, Schapire RE, Blair ME. 2017. Opening the black box: an open-source release of Maxent. Ecography. 40:887–893.
  • Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol. 53:793–808.
  • Provan J, Bennett KD. 2008. Phylogeographic insights into cryptic glacial refugia. Trends Ecol Evol. 23:564–571.
  • Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 67:901–904.
  • Ramírez-Soriano A, Ramos-Onsins SE, Rozas J, Calafell F, Navarro A. 2008. Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination. Genetics. 179:555–567.
  • Raupach MJ, Astrin JJ, Hannig K, Peters MK, Stoeckle MY, Wägele JW. 2010. Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes. Front Zool. 7:26.
  • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574.
  • Ryder OA, McLaren A, Brenner S, Zhang YP, Benirschke K. 2000. DNA banks for endangered animal species. Science. 288:275–277.
  • Schneider S, Excoffier L. 1999. 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.
  • 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. Ann Entomol Soc Am. 87:651–701.
  • Šípek P, Janšta P, Král D. 2011. Immature stages of Euchirinae (Coleoptera: Scarabaeoidea): genera Cheirotonus and Propomacrus with comments on their phylogeny based on larval and adult characters. Invert Systematics. 25:282–302.
  • Slarkin M. 1985. Gene flow in natural populations. Annu Rev Ecol Syst. 16:393–430.
  • Song W, Cao LJ, Li BY, Gong YJ, Hoffmann AA, Wei SJ. 2018. Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest. BMC Evol Biol. 18:152.
  • Städler T, Haubold B, Merino C, Stephan W, Pfaffelhuber P. 2009. The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics. 182:205–216.
  • 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.
  • Ulyshen MD, Zachos LG, Stireman JO, III, Sheehan TN, Garrick RC. 2017. Insights into the ecology, genetics and distribution of Lucanus elaphus Fabricius (Coleoptera: Lucanidae), North America’s giant stag beetle. Insect Conserv Divers. 10:331–340.
  • Virgilio M, Backeljau T, Nevado B, De Meyer M. 2010. Comparative performances of DNA barcoding across insect orders. BMC Bioinf . 11:206.
  • Wei SJ, Cao LJ, Gong YJ, Shi BC, Wang S, Zhang F, Guo XJ, Wang YM, Chen XX. 2015. Population genetic structure and approximate Bayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) in its native range. Mol Ecol. 24:4094–4111.
  • Xu L, Li Q, Jiang C. 1996. Diversity of soil actinomycetes in Yunnan, China. Appl Env Microbiol. 62:244–248.
  • Yan F, Zhou W, Zhao H, Yuan Z, Wang Y, Jiang K, Jin J, Murphy RW, Che J, Zhang Y. 2013. Geological events play a larger role than P leistocene climatic fluctuations in driving the genetic structure of Q uasipaa boulengeri (A nura: D icroglossidae). Mol Ecol. 22:1120–1133.
  • Yi CH, Chen Y, He QJ, Zhou Y, Wang L, Chen XM. 2015. Morphometric characteristics Study on Cherirotonus gestroi Pouillaud. J Northwest For Univ. 30:154–157.
  • Young RM. 1989. Euchirinae (Coleoptera: Scarabaeidae) of the world: distribution and taxonomy. Coleopt Bull. 43:205–236.
  • Zhan S, Zhang W, Niitepold K, Hsu J, Haeger JF, Zalucki MP, Altizer S, De Roode JC, Reppert SM, Kronforst MR. 2014. The genetics of monarch butterfly migration and warning colouration. Nature. 514:317–321.
  • Zhang SQ, Che LH, Li Y, Liang D, Pang H, Ślipiński A, Zhang P. 2018. Evolutionary history of Coleoptera revealed by extensive sampling of genes and species. Nat Commun. 9:205.
  • Zhao J, Shi Y, Wang J. 2011. Comparison between Quaternary Glaciations in China and the Marine Oxygen Isotope Stage (MIS): an improved schema. Acta Geogr Sin. 66:867–884.
  • Zhu Z, Ye H, Zhang Z. 2005. Genetic relationships among four Bactrocera cucurbitae geographic populations in Yunan province. Ying Yong Sheng Tai Xue Bao J Appl Ecol. 16:1889–1892.
  • Zhu H, Zhou S, Yan L, Shi J, Shen Y. 2019. Studies on the Evergreen Broad-leaved Forests of Yunnan, Southwestern China. Bot Rev. 85:131–148.

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.