| Literature DB >> 23404314 |
Kjersti S Kvie1, Silje Hogner, Leif Aarvik, Jan T Lifjeld, Arild Johnsen.
Abstract
Deep sympatric intraspecific divergence in mtDNA may reflect cryptic species or formerly distinct lineages in the process of remerging. Preliminary results from DNA barcoding of Scandinavian butterflies and moths showed high intraspecific sequence variation in the autumnal moth, Epirrita autumnata. In this study, specimens from different localities in Norway and some samples from Finland and Scotland, with two congeneric species as outgroups, were sequenced with mitochondrial and nuclear markers to resolve the discrepancy found between mtDNA divergence and present species-level taxonomy. We found five COI sub-clades within the E. autumnata complex, most of which were sympatric and with little geographic structure. Nuclear markers (ITS2 and Wingless) showed little variation and gave no indications that E. autumnata comprises more than one species. The samples were screened with primers for Wolbachia outer surface gene (wsp) and 12% of the samples tested positive. Two Wolbachia strains were associated with different mtDNA sub-clades within E. autumnata, which may indicate indirect selection/selective sweeps on haplotypes. Our results demonstrate that deep mtDNA divergences are not synonymous with cryptic speciation and this has important implications for the use of mtDNA in species delimitation, like in DNA barcoding.Entities:
Keywords: DNA barcoding; Epirrita autumnata; Wolbachia; mtDNA; nDNA; selective sweep
Year: 2012 PMID: 23404314 PMCID: PMC3568849 DOI: 10.1002/ece3.434
Source DB: PubMed Journal: Ecol Evol ISSN: 2045-7758 Impact factor: 2.912
Figure 1The study species, Epirrita autumnata. Photo: Svein Bekkum.
Information about the samples surveyed in this study, sampling locations, coordinates and collecting dates. Footnotes behind the municipalities show how the Norwegian E. autumnata samples were grouped into four Norwegian regions (used in the AMOVA)
| Tissue sample | Species | Country | Municipality | Coordinates | Collecting date |
|---|---|---|---|---|---|
| NHMO Lep08305 | Norway | Sør-Varanger | 69°33′48.53″N, 30°05′11.19″E | 10-20.VIII.2008 | |
| NHMO Lep08306 | Norway | Sør-Varanger | 69°27′09.34″N, 30°03′28.97″E | 9.IX-2.X.2008 | |
| NHMO Lep08307 | Norway | Sør-Varanger | 69°33′48.53″N, 30°05′11.19″E | 10-20.VIII.2008 | |
| NHMO Lep08308 | Norway | Sør-Varanger | 69°33′48.53″N, 30°05′11.19″E | 10-20.VIII.2008 | |
| RVO009 | Norway | Sør-Varanger | 69°22′14.45″N,29°40′43.56″E | 3.VIII-25.IX.2006 | |
| NHMO Lep08297 | Norway | Lierne | 64°26′44.32″N, 13°42′57.43″E | 25.IX.2008 | |
| NHMO Lep08298 | Norway | Lierne | 64°26′44.32″N, 13°42′57.43″E | 25.IX.2008 | |
| NHMO Lep08283 | Norway | Hol | 60°31′33.79″N, 8°18′21.14″E | 5-7.IX.2008 | |
| NHMO Lep08284 | Norway | Hol | 60°31′33.79″N, 8°18′21.14″E | 5-7.IX.2008 | |
| NHMO Lep08285 | Norway | Hol | 60°31′33.79″N, 8°18′21.14″E | 5-7.IX.2008 | |
| NHMO Lep08286 | Norway | Hol | 60°31′33.79″N, 8°18′21.14″E | 5-7.IX.2008 | |
| RVO014 | Norway | Nøtterøy | 59°12′20.38″N, 10°33′49.53″E | 5.VIII.2006 | |
| KB09008 | Norway | Oslo | 59°53′52.18″N, 10°43′55.37″E | 4-23.IX.2008 | |
| KB09009 | Norway | Oslo | 59°53′52.18″N, 10°43′55.37″E | 21.VIII-4.IX.2008 | |
| NHMO Lep09111 | Norway | Hobøl | 59°38′30.02″N, 10°59′50.52″E | 25-26.IX.2009 | |
| KB09016 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | IX.2007 | |
| KBE07032 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07033 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07034 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07035 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07036 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07037 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07038 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07039 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07040 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07041 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07042 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| KBE07043 | Norway | Vang | 61°09′29.51″N, 8°31′40.88″E | 1.IX.2006 | |
| NHMO Lep07087 | Norway | Ås | 60°04′02.28″N, 10°11′15.06″E | 27.IX.2007 | |
| KB08011 | Norway | Lillesand | 58°11′07.17″N,8°13′58.90″E | 4.X.2007 | |
| KB08012 | Norway | Lillesand | 58°11′07.17″N,8°13′58.90″E | X.2007 | |
| KB08013,5 | Norway | Åseral | 58°47′11.51″N,7°19′12.63″E | 11.X.2007 | |
| KB08092 | Norway | Søgne | 58°07′37.47″N,7°36′40.09″E | 7.X.2008 | |
| KB08093 | Norway | Søgne | 58°07′37.47″N,7°36′40.09″E | 17.X.2008 | |
| KB08094 | Norway | Søgne | 58°07′37.47″N,7°36′40.09″E | 17.X.2008 | |
| KB08095 | Norway | Søgne | 58°07′37.47″N,7°36′40.09″E | 17.X.2008 | |
| KB09097 | Norway | Søgne | 58°07′37.47″N,7°36′40.09″E | 17.X.2008 | |
| KB08083 | Norway | Kristiansand | 58°09′39.95″N, 8°05′57.44″E | 29.IX.2008 | |
| KB08086 | Norway | Kristiansand | 58°09′39.95″N, 8°05′57.44″E | 6.X.2008 | |
| KB08087 | Norway | Kristiansand | 58°12′08.76″N, 8°06′05.92″E | 12.X.2008 | |
| KB08101 | Norway | Kristiansand | 58°12′08.76″N, 8°06′05.92″E | 18.X.2008 | |
| KB09103 | Norway | Kristiansand | 58°12′08.76″N, 8°06′05.92″E | 12.X.2008 | |
| KB09004 | Norway | Årdal | 61°21′19.81″N,7°52′47.72″E | 5-15.IX.2008 | |
| KB09005 | Norway | Årdal | 61°21′19.81″N,7°52′47.72″E | 5-15.IX.2008 | |
| KB09020 | Norway | Årdal | 61°21′19.81″N,7°52′47.72″E | IX.2008 | |
| KB09021 | Norway | Årdal | 61°21′19.81″N,7°52′47.72″E | IX.2008 | |
| KB09023 | Norway | Årdal | 61°21′19.81″N,7°52′47.72″E | IX.2008 | |
| KB09024 | Norway | Årdal | 61°21′19.81″N,7°52′47.72″E | X.2008 | |
| KB09025 | Norway | Årdal | 61°21′19.81″N,7°52′47.72″E | X.2008 | |
| KB09026 | Norway | Årdal | 61°21′19.81″N,7°52′47.72″E | X.2008 | |
| KB09027 | Norway | Årdal | 61°21′19.81″N,7°52′47.72″E | X.2008 | |
| KB09028 | Norway | Årdal | 61°21′19.81″N,7°52′47.72″E | X.2008 | |
| RVO021 | Norway | Suldal | 59°29′49.34″N, 6°15′30.65E” | 2.X.2002 | |
| RVO010 | Norway | Suldal | 59°32′50.25″N,6°23′13.76″E | 18.X.2004 | |
| RVO011 | Norway | Suldal | 59°39′27.09″N,6°52′06.80″E | 24.X.2002 | |
| RVO013 | Norway | Klepp | 58°44′23.49″N, 5°30′45.48″E | 14.X.2001 | |
| RVO015 | Norway | Nøttery | 59°12′20.38″N, 10°33′49.53″E | IX.2006 | |
| RVO016 | Norway | Nøttery | 59°12′20.38″N, 10°33′49.53″E | IX.2006 | |
| RVO001 | Norway | Skien | 59°08′00.51″N, 9°39′25.22″E | 11.IX.2008 | |
| RVO002 | Norway | Skien | 59°08′00.51″N, 9°39′25.22″E | 11.IX.2008 | |
| RVO003 | Norway | Skien | 59°08′00.51″N, 9°39′25.22″E | 11.IX.2008 | |
| RVO004 | Norway | Skien | 59°08′00.51″N, 9°39′25.22″E | 11.IX.2008 | |
| RVO005 | Norway | Skien | 59°08′00.51″N, 9°39′25.22″E | 11.IX.2008 | |
| RVO007 | Norway | Skien | 59°08′00.51″N, 9°39′25.22″E | 11.IX.2008 | |
| RVO008 | Norway | Skien | 59°08′00.51″N, 9°39′25.22″E | 11.IX.2008 | |
| KB09033 | Norway | Årdal | 61°21′19.81″N, 7°52′47.72″E | 17.X.2008 | |
| KBE08098 | Norway | Kristiansand | 58°09′39.95″N, 8°05′57.44″E | 18.X.2008 | |
| KBE08100 | Norway | Kristiansand | 58°12′08.76″N, 8°06′05.92″E | 18.XI.2008 | |
| NHMO Lep09112 | Norway | Asker | 59°50′10.26″N, 10°28′01.80″E | 1.X.2009 | |
| NHMO Lep09113 | Norway | Asker | 59°50′10.26″N, 10°28′01.80″E | 1.X.2009 | |
| NHMO Lep09114 | Norway | Asker | 59°50′10.26″N, 10°28′01.80″E | 1.X.2009 | |
| NHMO Lep07088 | Norway | Ås | 60°04′02.28″N, 10°11′15.06″E | 27.IX.2007 | |
| KBE07046 | Norway | Lillesand | 58°11′07.17″N,8°13′58.90″E | 30.IX.2007 | |
| KB08102 | Norway | Kristiansand | 58°12′08.76″N, 8°06′05.92″E | 28.X.2008 | |
| KBE08096 | Norway | Kristiansand | 58°12′08.76″N, 8°06′05.92″E | 18.X.2008 | |
| KBE08097 | Norway | Kristiansand | 58°12′08.76″N, 8°06′05.92″E | 18.X.2008 | |
| KBE08099 | Norway | Kristiansand | 58°12′08.76″N, 8°06′05.92″E | 18.X.2008 | |
| RVO012 | Norway | Kristiansand | 58°04′06.92″N, 7°58′52.55″E | 1.XI.1999 | |
| KBE07047 | Norway | Lillesand | 58°11′07.17″N,8°13′58.90″E | 14.X.2007 | |
| NHMO Lep09105 | Finland | Lohja | 60°15′01.16″N, 24°04′45.68″E | 29.IX.2008 | |
| NHMO Lep09106 | Finland | Lohja | 60°15′01.16″N, 24°04′45.68″E | 29.IX.2008 | |
| NHMO Lep09107 | Finland | Lohja | 60°15′01.16″N, 24°04′45.68″E | 29.IX.2008 | |
| NHMO Lep09108 | Finland | Hyvinkââ | 60°37′54.63″N, 24°51′51.13″E | 8.X.2008 | |
| NHMO Lep09109 | Finland | Lohja | 60°15′01.16″N, 24°04′45.68″E | 29.IX.2008 | |
| NHMO Lep09118 | Scotland | Banffshire | 57°25′11.28″N, 2°38′35.08″V | 18.X.2009 | |
| NHMO Lep09119 | Scotland | Banffshire | 57°25′11.28″N, 2°38′35.08″V | 18.X.2009 | |
| NHMO Lep09120 | Scotland | Banffshire | 57°25′11.28″N, 2°38′35.08″V | 18.X.2009 |
North.
East.
South.
West.
Figure 2(a) Neighbor-joining analysis of 86 Epirrita samples based on the COI gene (Tamura 3-parameter used as substitution model). E. dilutata and E. christyi are included as out-groups. The five monophyletic groups of distinct E. autumnata haplotypes show high intraspecific variation. Bootstrap support (10000 iterations) is shown at each node. (b) Neighbor-joining analysis based on the wsp gene (Tamura 3-parameter used as substitution model). Bootstrap support (10000 iterations) is indicated at each node. Infections caused by bacteria represented in wsp group 1 are found in E. christyi. Infections from wsp group 2 are found in E. autumnata haplogroup 5, while infections represented in wsp group 3 are found in E. autumnata group 1 and 4. For each clade, we have added a representative wsp sequence (downloaded from Genbank) that has been identified in other Lepidoptera species (Eurema hecabe subsp. polygraphus).
Polymorphism statistics for Epirrita autumnata (and Epirrita christyi and Epirrita dilutata for COI) from the COI, Wingless and ITS2 region, and from Wolbachia outer surface gene (wsp)
| Species | N | L | Tajima's D | π | θ | |
|---|---|---|---|---|---|---|
| COI | 62 | 658 | -0.77659 | 0.01674 | 0.02043 | |
| 18 | 658 | -0.89359 | 0.00693 | 0.00907 | ||
| 6 | 658 | -0.93302 | 0.00058 | 0.00076 | ||
| Wingless | 14 | 409 | -1.15524 | 0.00039 | 0.00085 | |
| ITS2 | 23 | 484 | 1.99999 | 0.00285 | 0.542 | |
| 17 | 564 | -0.93302 | 0.10812 | 0.06573 |
Number of individuals.
Sequence length.
None of the D values significant.
Average pairwise sequence difference per nucleotide (Nei 1987).
Expected heterozygosity per nucleotide (Watterson 1975).
Genetic distance (Tamura 3-parameter) between the five Epirrita autumnata haplotype groups 1-5 (below diagonal) with standard errors (above diagonal)
| E. a 1 | E. a 2 | E. a 3 | E. a 4 | E. a 5 | |
|---|---|---|---|---|---|
| 0.005 | 0.007 | 0.009 | 0.010 | ||
| 0.015 | 0.007 | 0.008 | 0.009 | ||
| 0.023 | 0.022 | 0.009 | 0.009 | ||
| 0.035 | 0.033 | 0.039 | 0.009 | ||
| 0.041 | 0.036 | 0.040 | 0.037 |
Figure A1Minimum evolution analysis (Tamura 3-parameter as substitution model) of the COI data set (n = 86), showing the same structure as the NJ analysis, with 5 distinct COI-haplotypes. Bootstrap (10000 iterations) is shown at each node.
Figure A2Maximum parsimony analysis (using the complete deletion option) of the COI data set (n = 86). MP analysis also shows high intraspecific variation within E. autumnata. Bootstrap values (500 iterations) are shown at each node.
Figure 3Neighbor-joining analysis of 27 Epirrita sequences based on the ITS2 gene (Jukes–Cantor used as substitution model). E. christyi and E. dilutata are included as out-groups. E. autumnata are shown as one monophyletic group with some diversity (< 0.5%). Bootstrap support (10000 iterations) is shown at each node.
Figure 4Neighbor-joining analysis of 20 Epirrita sequences based on the Wingless gene and with E. christyi as out-group (Jukes–Cantor used as substitution model). Bootstrap support (10,000 iterations) is shown at each node.
AMOVA of Norwegian Epirrita autumnata samples showing haplotype distribution in four selected regions in Norway; north, east, south, and west
| Source of variation | d.f | Sum of squares | Variance components | Percentage of variation |
|---|---|---|---|---|
| Among regions | 3 | 14.444 | 0.069 Va | 1.710 |
| Within regions | 49 | 194.273 | 3.965 Vb | 98.290 |
| Total | 52 | 208.717 | 4.034 |
GenBank accession numbers
| Tissue sample | Species | COI | ITS2 | Wingless | |
|---|---|---|---|---|---|
| NHMO Lep08305 | JX260769 | JN225585 | JN225572 | ||
| NHMO Lep08306 | JX260785 | JN225586 | JN225573 | ||
| NHMO Lep08307 | JX260741 | JN225587 | JN225566 | ||
| NHMO Lep08308 | JX260738 | JN225588 | JN225581 | ||
| RVO009 | JX260749 | JN225606 | JN225568 | JX310341 | |
| NHMO Lep08297 | JX260733 | ||||
| NHMO Lep08298 | JX260786 | ||||
| NHMO Lep08283 | JX260759 | JN225584 | JN225571 | ||
| NHMO Lep08284 | JX260775 | ||||
| NHMO Lep08285 | JX260783 | ||||
| NHMO Lep08286 | JX260782 | ||||
| RVO014 | JX260772 | JN225590 | JN225575 | ||
| KB09008 | JX260758 | JN22600 | |||
| KB09009 | JX260768 | JN225601 | |||
| NHMO Lep09111 | JX260754 | ||||
| KB09016 | JX260757 | ||||
| KBE07032 | JX260784 | ||||
| KBE07033 | JX260739 | ||||
| KBE07034 | JX260760 | ||||
| KBE07035 | JX260762 | ||||
| KBE07036 | JX260752 | ||||
| KBE07037 | JX260771 | ||||
| KBE07038 | JX260773 | ||||
| KBE07039 | JX260789 | ||||
| KBE07040 | JX260788 | ||||
| KBE07041 | JX260756 | ||||
| KBE07042 | JX260743 | ||||
| KBE07043 | JX260753 | ||||
| NHMO Lep07087 | JX260779 | ||||
| KB08011 | JX269737 | JN225592 | JN225580 | ||
| KB08012 | JX260787 | JX310345 | |||
| KB08013,5 | JX260778 | ||||
| KB08092 | JX260745 | ||||
| KB08093 | JX260736 | JN225595 | JX310346 | ||
| KB08094 | JX260744 | JN225596 | JN225567 | ||
| KB08095 | JX260742 | ||||
| KB09097 | JX260780 | JN225604 | |||
| KB08083 | JX260770 | ||||
| KB08086 | JX260751 | ||||
| KB08087 | JX260791 | JN225593 | JN225577 | JX310342 | |
| KB08101 | JX260746 | ||||
| KB09103 | JX260740 | JN225605 | JN225569 | JX310340 | |
| KB09004 | JX260731 | ||||
| KB09005 | JX260761 | ||||
| KB09020 | JX260790 | ||||
| KB09021 | JX260765 | ||||
| KB09023 | JX260767 | ||||
| KB09024 | JX260766 | ||||
| KB09025 | JX260792 | ||||
| KB09026 | JX260774 | JN225602 | JN225578 | ||
| KB09027 | JX260734 | JN225603 | |||
| KB09028 | JX260732 | ||||
| RVO021 | JX260747 | JN225591 | JN225576 | ||
| RVO010 | JX260710 | JN225589 | JN225574 | JX310348 | |
| RVO011 | JX260781 | ||||
| RVO013 | JX260808 | ||||
| RVO015 | JX260796 | ||||
| RVO016 | JX260802 | ||||
| RVO001 | JX260800 | ||||
| RVO002 | JX260806 | ||||
| RVO003 | JX260794 | ||||
| RVO004 | JX260807 | JN225607 | JN225582 | ||
| RVO005 | JX260793 | JN225608 | JN225583 | ||
| RVO007 | JX260799 | JX310336 | |||
| RVO008 | JX260797 | ||||
| KB09033 | JX260804 | ||||
| KBE08098 | JX260809 | ||||
| KBE08100 | JX260805 | JX310335 | |||
| NHMO Lep09112 | JX260803 | JX310337 | |||
| NHMO Lep09113 | JX260810 | JX310338 | |||
| NHMO Lep09114 | JX260795 | JX310339 | |||
| NHMO Lep07088 | JX260798 | ||||
| KBE07046 | JX260801 | ||||
| KB08102 | JX260814 | JN225610 | |||
| KBE08096 | JX260813 | ||||
| KBE08097 | JX260816 | JN225609 | |||
| KBE08099 | JX260812 | ||||
| RVO012 | JX260811 | ||||
| KBE07047 | JX260815 | ||||
| NHMO Lep09105 | JX260764 | JN225594 | JN225570 | JX310347 | |
| NHMO Lep09106 | JX260735 | ||||
| NHMO Lep09107 | JX260763 | ||||
| NHMO Lep09108 | JX260748 | JX310343 | |||
| NHMO Lep09109 | JX260777 | JX310344 | |||
| NHMO Lep09118 | JX260750 | JN225598 | |||
| NHMO Lep09119 | JN225599 | JN225579 | |||
| NHMO Lep09120 | JX260776 | JN225597 |