1
|
Wang H, Zhong X, Lin H, Li S, Yi J, Zhang G, Liu X, Gu L. Genetic Diversity and Population Structure of Gynaephora qinghaiensis in Yushu Prefecture, Qinghai Province Based on the Mitochondrial COI Gene. Biochem Genet 2021; 59:1396-1412. [PMID: 33891260 DOI: 10.1007/s10528-021-10065-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
Abstract
Gynaephora qinghaiensis (Lepidoptera: Lymantriidae: Gynaephora), a serious economic pest in alpine meadows, is mainly distributed in Yushu prefecture, Qinghai province, China. In this study, we aimed to investigate the genetic diversity and population structure of G. qinghaiensis through analyzing the sequence of 194 mitochondrial cytochrome oxidase subunit (COI) genes (658 bp in length) identified from 10 geographic populations located in three different countries, including Zhiduo, Zaduo, and Chengduo, of Yushu prefecture. Eleven haplotypes were identified from all populations of G. qinghaiensis with high levels of haplotype diversity (0.78500) and low levels of nucleotide diversity (0.00511). High levels of genetic differentiation and low levels of gene flow were also detected among the populations of G. qinghaiensis. Analysis of molecular variance (AMOVA) showed that 90.13% of the variation was attributed to distribution among groups (Chengduo, Zhiduo, and Zaduo), and 5.22% and 4.65% were, respectively, attributed to distribution among populations, within group, and within populations. The result of mantel test showed a highly significant positive correlation (P < 0.01) between FST and geographical distance. A maximum likelihood tree showed that most haplotypes were grouped into three clusters corresponding to the three counties, suggesting a significant phylogeographic structure in the populations of G. qinghaiensis. The haplotype networks revealed that H2 may be the most primitive haplotype and the most adaptable in nature. Populations 7# and 8# had haplotype H2 and higher haplotype diversity; therefore, we speculated that the G. qinghaiensis in both populations were more adaptable to the environment and had greater outbreak potential and, therefore, should be focused on in terms of prevention and control. Our findings provide valuable information for further study of the population structure and phylogeny of G. qinghaiensis and provide a theoretical basis for the control of G. qinghaiensis.
Collapse
Affiliation(s)
- Haizhen Wang
- Department of Life Sciences, Luliang University, Luliang, Shanxi, China
| | - Xin Zhong
- Food and Health Engineering Research Center of State Education Ministry, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Huafeng Lin
- Department of Biotechnology, College of Life Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China
| | - Shaosong Li
- The Bureau of Health of Longhua, Shenzhen, Guangdong, China
| | - Jiequn Yi
- Guangzhou Sugarcane Industry Research Institute, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Guren Zhang
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xin Liu
- Food and Health Engineering Research Center of State Education Ministry, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China.
| | - Li Gu
- Food and Health Engineering Research Center of State Education Ministry, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China.
| |
Collapse
|
2
|
DNA barcoding and species delimitation of butterflies (Lepidoptera) from Nigeria. Mol Biol Rep 2020; 47:9441-9457. [PMID: 33200313 DOI: 10.1007/s11033-020-05984-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/05/2020] [Indexed: 10/23/2022]
Abstract
Accurate identification of species is a prerequisite for successful biodiversity management and further genetic studies. Species identification techniques often require both morphological diagnostics and molecular tools, such as DNA barcoding, for correct identification. In particular, the use of the subunit I of the mitochondrial cytochrome c oxidase (COI) gene for DNA barcoding has proven useful in species identification for insects. However, to date, no studies have been carried out on the DNA barcoding of Nigerian butterflies. We evaluated the utility of DNA barcoding applied for the first time to 735 butterfly specimens from southern Nigeria. In total, 699 DNA barcodes, resulting in a record of 116 species belonging to 57 genera, were generated. Our study sample comprised 807 DNA barcodes based on sequences generated from our current study and 108 others retrieved from BOLD. Different molecular analyses, including genetic distance-based evaluation (Neighbor-Joining, Maximum Likelihood and Bayesian trees) and species delimitation tests (TaxonDNA, Automated Barcode Gap Discovery, General Mixed Yule-Coalescent, and Bayesian Poisson Tree Processes) were performed to accurately identify and delineate species. The genetic distance-based analyses resulted in 163 well-separated clusters consisting of 147 described and 16 unidentified species. Our findings indicate that about 90.20% of the butterfly species were explicitly discriminated using DNA barcodes. Also, our field collections reported the first country records of ten butterfly species-Acraea serena, Amauris cf. dannfelti, Aterica galena extensa, Axione tjoane rubescens, Charaxes galleyanus, Papilio lormieri lormeri, Pentila alba, Precis actia, Precis tugela, and Tagiades flesus. Further, DNA barcodes revealed a high mitochondrial intraspecific divergence of more than 3% in Bicyclus vulgaris vulgaris and Colotis evagore. Furthermore, our result revealed an overall high haplotype (gene) diversity (0.9764), suggesting that DNA barcoding can provide information at a population level for Nigerian butterflies. The present study confirms the efficiency of DNA barcoding for identifying butterflies from Nigeria. To gain a better understanding of regional variation in DNA barcodes of this biogeographically complex area, future work should expand the DNA barcode reference library to include all butterfly species from Nigeria as well as surrounding countries. Also, further studies, involving relevant genetic and eco-morphological datasets, are required to understand processes governing mitochondrial intraspecific divergences reported in some species complexes.
Collapse
|
3
|
Marabuto E, Pina-Martins F, Rebelo MT, Paulo OS. Ancient divergence, a crisis of salt and another of ice shaped the evolution of the west Mediterranean butterfly Euchloe tagis. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractThe Mediterranean region is an extremely complex hotspot where, since the Miocene, extensive geological, habitat and climate changes have taken place, alternating between warm and cold periods. These phenomena have taken a toll on the genetic composition of species, and surviving lineages have often adapted locally and diverged to the point of (complete) speciation. To study these phenomena, in this study we used one of the most enigmatic butterflies, the Portuguese dappled white, Euchloe tagis, a west Mediterranean endemic with fragmented, morphologically differentiated populations whose status have long been disputed. Even its affiliations with other Anthocharidini are largely unresolved. We used mitochondrial and nuclear markers under a phylogenetic and phylogeographical framework to evaluate its placement among relatives and population differentiation, reconstructing its evolutionary history. We found that this species had a Miocene origin ~15 Mya and was nearest to Euchloe s.s. and Elphinstonia. Its populations showed high genetic diversity but all coalesced to 5.3 Mya, when European and all but one African population diverged. Our multiple findings concerning the evolution of E. tagis through a changing, narrow habitable area might provide a more general perspective on how species survive within this hotspot of paramount importance.
Collapse
Affiliation(s)
- Eduardo Marabuto
- Computational Biology and Population Genomics Group, cE3c – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Francisco Pina-Martins
- Computational Biology and Population Genomics Group, cE3c – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Maria Teresa Rebelo
- Centre for Environmental and Marine Studies (CESAM), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| |
Collapse
|
4
|
Debode F, Marien A, Gérard A, Francis F, Fumière O, Berben G. Development of real-time PCR tests for the detection of Tenebrio molitor in food and feed. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2017; 34:1421-1426. [DOI: 10.1080/19440049.2017.1320811] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Frédéric Debode
- Unit Traceability and Authentication, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
| | - Aline Marien
- Unit Traceability and Authentication, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
- European Union Reference Laboratory for Animal Proteins in feedingstuffs (EURL-AP), Gembloux, Belgium
| | - Amaury Gérard
- Unit Traceability and Authentication, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech – University of Liège (ULg), Gembloux, Belgium
| | - Frédéric Francis
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech – University of Liège (ULg), Gembloux, Belgium
| | - Olivier Fumière
- Unit Traceability and Authentication, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
- European Union Reference Laboratory for Animal Proteins in feedingstuffs (EURL-AP), Gembloux, Belgium
| | - Gilbert Berben
- Unit Traceability and Authentication, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
- European Union Reference Laboratory for Animal Proteins in feedingstuffs (EURL-AP), Gembloux, Belgium
| |
Collapse
|
5
|
Fan X, Chiba H, Huang Z, Fei W, Wang M, Sáfián S. Clarification of the Phylogenetic Framework of the Tribe Baorini (Lepidoptera: Hesperiidae: Hesperiinae) Inferred from Multiple Gene Sequences. PLoS One 2016; 11:e0156861. [PMID: 27463803 PMCID: PMC4963138 DOI: 10.1371/journal.pone.0156861] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 05/21/2016] [Indexed: 11/18/2022] Open
Abstract
Members of the skipper tribe Baorini generally resemble each other and are characterized by dark brown wings with hyaline white spots. These shared characteristics have caused difficulties with revealing the relationships among genera and species in the group, and some conflicting taxonomic views remain unresolved. The present study aims to infer a more comprehensive phylogeny of the tribe using molecular data, to test the monophyly of the tribe as well as the genera it includes in order to clarify their taxonomic status, and finally to revise the current classification of the group. In order to reconstruct a phylogenetic tree, the mitochondrial COI-COII and 16S genes as well as the nuclear EF-1α and 28S genes were analyzed using parsimony, maximum likelihood, and Bayesian inference. The analysis included 67 specimens of 41 species, and we confirmed the monophyly of Baorini, and revealed that 14 genera are well supported. The genus Borbo is separated into three clades: Borbo, Pseudoborbo, and Larsenia gen. nov. We confirmed that Polytremis is polyphyletic and separated into three genera: Polytremis, Zinaida, and Zenonoida gen. nov., and also confirmed that the genus Prusiana is a member of the tribe. Relationships among some genera were strongly supported. For example, Zenonia and Zenonoida were found to be sister taxa, closely related to Zinaida and Iton, while Pelopidas and Baoris were also found to cluster together.
Collapse
Affiliation(s)
- Xiaoling Fan
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Hideyuki Chiba
- B. P. Bishop Museum, Honolulu, Hawaii, United States of America
| | - Zhenfu Huang
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Wen Fei
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Min Wang
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Szabolcs Sáfián
- Institute of Silviculture and Forest Protection, University of West Hungary, Sopron, Hungary
| |
Collapse
|
6
|
Yang M, Zhang Y. Phylogenetic utility of ribosomal genes for reconstructing the phylogeny of five Chinese satyrine tribes (Lepidoptera, Nymphalidae). Zookeys 2015:105-20. [PMID: 25878526 PMCID: PMC4389127 DOI: 10.3897/zookeys.488.9171] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 03/05/2015] [Indexed: 01/09/2023] Open
Abstract
Satyrinae is one of twelve subfamilies of the butterfly family Nymphalidae, which currently includes nine tribes. However, phylogenetic relationships among them remain largely unresolved, though different researches have been conducted based on both morphological and molecular data. However, ribosomal genes have never been used in tribe level phylogenetic analyses of Satyrinae. In this study we investigate for the first time the phylogenetic relationships among the tribes Elymniini, Amathusiini, Zetherini and Melanitini which are indicated to be a monophyletic group, and the Satyrini, using two ribosomal genes (28s rDNA and 16s rDNA) and four protein-coding genes (EF-1α, COI, COII and Cytb). We mainly aim to assess the phylogenetic informativeness of the ribosomal genes as well as clarify the relationships among different tribes. Our results show the two ribosomal genes generally have the same high phylogenetic informativeness compared with EF-1α; and we infer the 28s rDNA would show better informativeness if the 28s rDNA sequence data for each sampling taxon are obtained in this study. The placement of the monotypic genus Callarge Leech in Zetherini is confirmed for the first time based on molecular evidence. In addition, our maximum likelihood (ML) and Bayesian inference (BI) trees consistently show that the involved Satyrinae including the Amathusiini is monophyletic with high support values. Although the relationships among the five tribes are identical among ML and BI analyses and are mostly strongly-supported in BI analysis, those in ML analysis are lowly- or moderately- supported. Therefore, the relationships among the related five tribes recovered herein need further verification based on more sampling taxa.
Collapse
Affiliation(s)
- Mingsheng Yang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
7
|
SUTRISNO HARI. Phylogenetic Relationships Within Arctornis (Lepidoptera: Erebidae) Based on COI Gene Sequences. HAYATI JOURNAL OF BIOSCIENCES 2015. [DOI: 10.4308/hjb.22.1.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
8
|
Lei Y, Xu C, Xu C, Wang R. The complete mitochondrial genome of Celastrina hersilia (Lepidoptera: Lycaenidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:218-9. [PMID: 24495135 DOI: 10.3109/19401736.2014.880896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Celastrina hersilia (Lepidoptera: Lycaenidae) is determined in this work. The mitochondrial genome is 15,304 bp in length, which contains typical 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes and 1 non-coding A + T-rich region. All PCGs are initiated by ATA or ATT codons, except for COI, which uses CGA as a start codon. Four PCGs (COI, COII, ND5, and ND4) terminate with incomplete termination codons TA or T, while the others use TAA as stop codons. Most of the tRNA genes can be folded into a typical cloverleaf structure. The A + T-rich region is 370 bp in length, which contains several features common to the other lepidopteran species.
Collapse
Affiliation(s)
- Ying Lei
- a College of Life Sciences, Peking University , Beijing , P.R. China
| | - Chang Xu
- a College of Life Sciences, Peking University , Beijing , P.R. China
| | - Chongren Xu
- a College of Life Sciences, Peking University , Beijing , P.R. China
| | - Rongjiang Wang
- a College of Life Sciences, Peking University , Beijing , P.R. China
| |
Collapse
|
9
|
Hao JJ, Hao JS, Sun XY, Zhang LL, Yang Q. The complete mitochondrial genomes of the Fenton's wood white, Leptidea morsei, and the lemon emigrant, Catopsilia pomona. JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:130. [PMID: 25368074 PMCID: PMC4222323 DOI: 10.1093/jis/14.1.130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 06/05/2013] [Indexed: 06/04/2023]
Abstract
The complete mitochondrial genomes of Leptidea morsei Fenton (Lepidoptera: Pieridae: Dis-morphiinae) and Catopsilia pomona (F.) (Lepidoptera: Pieridae: Coliadinae) were determined to be 15,122 and 15,142 bp in length, respectively, with that of L. morsei being the smallest among all known butterflies. Both mitogenomes contained 37 genes and an A+T-rich region, with the gene order identical to those of other butterflies, except for the presence of a tRNA-like insertion, tRNA(Leu) (UUR), in C. pomona. The nucleotide compositions of both genomes were higher in A and T (80.2% for L. morsei and 81.3% for C. pomona) than C and G; the A+T bias had a significant effect on the codon usage and the amino acid composition. The protein-coding genes utilized the standard mitochondrial start codon ATN, except the COI gene using CGA as the initiation codon, as reported in other butterflies. The intergenic spacer sequence between the tRNA(Ser) (UCN) and ND1 genes contained the ATACTAA motif. The A+T-rich region harbored a poly-T stretch and a conserved ATAGA motif located at the end of the region. In addition, there was a triplicated 23 bp repeat and a microsatellite-like (TA)9(AT)3 element in the A+T-rich region of the L. morsei mitogenome, while in C. pomona, there was a duplicated 24 bp repeat element and a microsatellite-like (TA)9 element. The phylogenetic trees of the main butterfly lineages (Hesperiidae, Papilionidae, Pieridae, Nymphalidae, Lycaenidae, and Riodinidae) were reconstructed with maximum likelihood and Bayesian inference methods based on the 13 concatenated nucleotide sequences of protein-coding genes, and both trees showed that the Pieridae family is sister to Lycaenidae. Although this result contradicts the traditional morphologically based views, it agrees with other recent studies based on mitochondrial genomic data.
Collapse
Affiliation(s)
- Juan-Juan Hao
- College of Life Sciences, Anhui Normal University, 241000 Wuhu, China
| | - Jia-Sheng Hao
- College of Life Sciences, Anhui Normal University, 241000 Wuhu, China
| | - Xiao-Yan Sun
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lan-Lan Zhang
- College of Life Sciences, Anhui Normal University, 241000 Wuhu, China
| | - Qun Yang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| |
Collapse
|
10
|
Wilson JJ, Sing KW, Sofian-Azirun M. Building a DNA barcode reference library for the true butterflies (Lepidoptera) of Peninsula Malaysia: what about the subspecies? PLoS One 2013; 8:e79969. [PMID: 24282514 PMCID: PMC3839974 DOI: 10.1371/journal.pone.0079969] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 10/07/2013] [Indexed: 11/26/2022] Open
Abstract
The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92%) and revealed that most subspecies possessed unique DNA barcodes (84%). In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity.
Collapse
Affiliation(s)
- John-James Wilson
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kong-Wah Sing
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Sofian-Azirun
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
11
|
Description of new mitochondrial genomes (Spodoptera litura, Noctuoidea and Cnaphalocrocis medinalis, Pyraloidea) and phylogenetic reconstruction of Lepidoptera with the comment on optimization schemes. Mol Biol Rep 2013; 40:6333-49. [PMID: 24057247 DOI: 10.1007/s11033-013-2748-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
Abstract
We newly sequenced mitochondrial genomes of Spodoptera litura and Cnaphalocrocis medinalis belonging to Lepidoptera to obtain further insight into mitochondrial genome evolution in this group and investigated the influence of optimal strategies on phylogenetic reconstruction of Lepidoptera. Estimation of p-distances of each mitochondrial gene for available taxonomic levels has shown the highest value in ND6, whereas the lowest values in COI and COII at the nucleotide level, suggesting different utility of each gene for different hierarchical group when individual genes are utilized for phylogenetic analysis. Phylogenetic analyses mainly yielded the relationships (((((Bombycoidea + Geometroidea) + Noctuoidea) + Pyraloidea) + Papilionoidea) + Tortricoidea), evidencing the polyphyly of Macrolepidoptera. The Noctuoidea concordantly recovered the familial relationships (((Arctiidae + Lymantriidae) + Noctuidae) + Notodontidae). The tests of optimality strategies, such as exclusion of third codon positions, inclusion of rRNA and tRNA genes, data partitioning, RY recoding approach, and recoding nucleotides into amino acids suggested that the majority of the strategies did not substantially alter phylogenetic topologies or nodal supports, except for the sister relationship between Lycaenidae and Pieridae only in the amino acid dataset, which was in contrast to the sister relationship between Lycaenidae and Nymphalidae in Papilionoidea in the remaining datasets.
Collapse
|
12
|
Ashfaq M, Akhtar S, Khan AM, Adamowicz SJ, Hebert PDN. DNA barcode analysis of butterfly species from Pakistan points towards regional endemism. Mol Ecol Resour 2013; 13:832-43. [PMID: 23789612 PMCID: PMC3910150 DOI: 10.1111/1755-0998.12131] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 05/24/2013] [Accepted: 05/28/2013] [Indexed: 02/06/2023]
Abstract
DNA barcodes were obtained for 81 butterfly species belonging to 52 genera from sites in north-central Pakistan to test the utility of barcoding for their identification and to gain a better understanding of regional barcode variation. These species represent 25% of the butterfly fauna of Pakistan and belong to five families, although the Nymphalidae were dominant, comprising 38% of the total specimens. Barcode analysis showed that maximum conspecific divergence was 1.6%, while there was 1.7–14.3% divergence from the nearest neighbour species. Barcode records for 55 species showed <2% sequence divergence to records in the Barcode of Life Data Systems (BOLD), but only 26 of these cases involved specimens from neighbouring India and Central Asia. Analysis revealed that most species showed little incremental sequence variation when specimens from other regions were considered, but a threefold increase was noted in a few cases. There was a clear gap between maximum intraspecific and minimum nearest neighbour distance for all 81 species. Neighbour-joining cluster analysis showed that members of each species formed a monophyletic cluster with strong bootstrap support. The barcode results revealed two provisional species that could not be clearly linked to known taxa, while 24 other species gained their first coverage. Future work should extend the barcode reference library to include all butterfly species from Pakistan as well as neighbouring countries to gain a better understanding of regional variation in barcode sequences in this topographically and climatically complex region.
Collapse
Affiliation(s)
- Muhammad Ashfaq
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada, N1G 2W1.
| | | | | | | | | |
Collapse
|
13
|
Stoeckle MY, Coffran C. TreeParser-aided Klee diagrams display taxonomic clusters in DNA barcode and nuclear gene datasets. Sci Rep 2013; 3:2635. [PMID: 24022383 PMCID: PMC3769653 DOI: 10.1038/srep02635] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/23/2013] [Indexed: 01/08/2023] Open
Abstract
Indicator vector analysis of a nucleotide sequence alignment generates a compact heat map, called a Klee diagram, with potential insight into clustering patterns in evolution. However, so far this approach has examined only mitochondrial cytochrome c oxidase I (COI) DNA barcode sequences. To further explore, we developed TreeParser, a freely-available web-based program that sorts a sequence alignment according to a phylogenetic tree generated from the dataset. We applied TreeParser to nuclear gene and COI barcode alignments from birds and butterflies. Distinct blocks in the resulting Klee diagrams corresponded to species and higher-level taxonomic divisions in both groups, and this enabled graphic comparison of phylogenetic information in nuclear and mitochondrial genes. Our results demonstrate TreeParser-aided Klee diagrams objectively display taxonomic clusters in nucleotide sequence alignments. This approach may help establish taxonomy in poorly studied groups and investigate higher-level clustering which appears widespread but not well understood.
Collapse
Affiliation(s)
- Mark Y. Stoeckle
- Program for the Human Environment, The Rockefeller University, New York, NY 10065
| | - Cameron Coffran
- Program for the Human Environment, The Rockefeller University, New York, NY 10065
| |
Collapse
|
14
|
Heikkilä M, Kaila L, Mutanen M, Peña C, Wahlberg N. Cretaceous origin and repeated tertiary diversification of the redefined butterflies. Proc Biol Sci 2012; 279:1093-9. [PMID: 21920981 PMCID: PMC3267136 DOI: 10.1098/rspb.2011.1430] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 08/23/2011] [Indexed: 11/12/2022] Open
Abstract
Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous-Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis, a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.
Collapse
Affiliation(s)
- Maria Heikkilä
- Finnish Museum of Natural History, University of Helsinki, PO Box 17, Helsinki 00014, Finland
| | - Lauri Kaila
- Finnish Museum of Natural History, University of Helsinki, PO Box 17, Helsinki 00014, Finland
| | - Marko Mutanen
- Zoological Museum, Department of Biology, University of Oulu, PO Box 3000, Oulu 90014, Finland
| | - Carlos Peña
- Laboratory of Genetics, Department of Biology, University of Turku, Turku 20014, Finland
| | - Niklas Wahlberg
- Laboratory of Genetics, Department of Biology, University of Turku, Turku 20014, Finland
| |
Collapse
|
15
|
Kim MJ, Kang AR, Jeong HC, Kim KG, Kim I. Reconstructing intraordinal relationships in Lepidoptera using mitochondrial genome data with the description of two newly sequenced lycaenids, Spindasis takanonis and Protantigius superans (Lepidoptera: Lycaenidae). Mol Phylogenet Evol 2011; 61:436-45. [DOI: 10.1016/j.ympev.2011.07.013] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 07/09/2011] [Accepted: 07/19/2011] [Indexed: 11/30/2022]
|