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Does the DNA barcoding gap exist? - a case study in blue butterflies (Lepidoptera: Lycaenidae).

ABSTRACT: BACKGROUND:DNA barcoding, i.e. the use of a 648 bp section of the mitochondrial gene cytochrome c oxidase I, has recently been promoted as useful for the rapid identification and discovery of species. Its success is dependent either on the strength of the claim that interspecific variation exceeds intraspecific variation by one order of magnitude, thus establishing a "barcoding gap", or on the reciprocal monophyly of species. RESULTS:We present an analysis of intra- and interspecific variation in the butterfly family Lycaenidae which includes a well-sampled clade (genus Agrodiaetus) with a peculiar characteristic: most of its members are karyologically differentiated from each other which facilitates the recognition of species as reproductively isolated units even in allopatric populations. The analysis shows that there is an 18% overlap in the range of intra- and interspecific COI sequence divergence due to low interspecific divergence between many closely related species. In a Neighbour-Joining tree profile approach which does not depend on a barcoding gap, but on comprehensive sampling of taxa and the reciprocal monophyly of species, at least 16% of specimens with conspecific sequences in the profile were misidentified. This is due to paraphyly or polyphyly of conspecific DNA sequences probably caused by incomplete lineage sorting. CONCLUSION:Our results indicate that the "barcoding gap" is an artifact of insufficient sampling across taxa. Although DNA barcodes can help to identify and distinguish species, we advocate using them in combination with other data, since otherwise there would be a high probability that sequences are misidentified. Although high differences in DNA sequences can help to identify cryptic species, a high percentage of well-differentiated species has similar or even identical COI sequences and would be overlooked in an isolated DNA barcoding approach.

SUBMITTER: Wiemers M

PROVIDER: S-EPMC1838910 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature

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Does the DNA barcoding gap exist? - a case study in blue butterflies (Lepidoptera: Lycaenidae).

Wiemers Martin M Fiedler Konrad K

Frontiers in zoology 20070307

<h4>Background</h4>DNA barcoding, i.e. the use of a 648 bp section of the mitochondrial gene cytochrome c oxidase I, has recently been promoted as useful for the rapid identification and discovery of species. Its success is dependent either on the strength of the claim that interspecific variation exceeds intraspecific variation by one order of magnitude, thus establishing a "barcoding gap", or on the reciprocal monophyly of species.<h4>Results</h4>We present an analysis of intra- and interspeci ...[more]

PMID: 17343734

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Project description:The Balkan Peninsula represents one of the hottest biodiversity spots in Europe. However, the invertebrate fauna of this region is still insufficiently investigated, even in respect of such well-studied organisms as Lepidoptera. Here we use a combination of chromosomal, molecular and morphological markers to rearrange the group of so-called anomalous blue butterflies (also known as 'brown complex' of the subgenus Agrodiaetus Hübner, [1822] and as the Polyommatus (Agrodiaetus) admetus (Esper, 1783) species group) and to reveal its cryptic taxonomic structure. We demonstrate that Polyommatus aroaniensis (Brown, 1976) is not as widespread in the Balkans as was previously thought. In fact, it has a dot-like distribution range restricted to the Peloponnese Peninsula in South Greece. Polyommatus orphicus Kolev, 2005 is not as closely related to the Turkish species Polyommatus dantchenkoi (Lukhtanov & Wiemers, 2003) as was supposed earlier. Instead, it is a Balkan endemic represented by two subspecies: Polyommatus orphicus orphicus (Bulgaria) and Polyommatus orphicus eleniae Coutsis & De Prins, 2005 (Northern Greece). Polyommatus ripartii (Freyer, 1830) is represented in the Balkans by an endemic subspecies Polyommatus ripartii pelopi. The traditionally recognized Polyommatus admetus (Esper, 1783) is shown to be a heterogeneous complex and is divided into Polyommatus admetus sensu stricto (the Balkans and west Turkey) and Polyommatus yeranyani (Dantchenko & Lukhtanov, 2005) (east Turkey, Armenia, Azerbaijan and Iran). Polyommatus nephohiptamenos (Brown & Coutsis, 1978) is confirmed to be a species with a dot-like distribution range in Northern Greece. Finally, from Central Greece (Timfristos and Parnassos mountains) we describe Polyommatus timfristos Lukhtanov, Vishnevskaya & Shapoval, sp. n. which differs by its haploid chromosome number (n=38) from the closely related and morphologically similar Polyommatus aroaniensis (n=47-48) and Polyommatus orphicus (n=41-42). We provide chromosomal evidence for three separate south Balkan Pleistocene refugia (Peloponnesse, Central Greece and Northern Greece/South Bulgaria) and stress the biogeographic importance of Central Greece as a place of diversification. Then we argue that the data obtained have direct implications for butterfly karyology, taxonomy, biogeography and conservation.

Project description:BackgroundCurrent molecular phylogenetic studies of Lepidoptera and most other arthropods are predominantly based on mitochondrial genes and a limited number of nuclear genes. The nuclear genes, however, generally do not provide sufficient information for young radiations. ITS2 , which has proven to be an excellent nuclear marker for similarly aged radiations in other organisms like fungi and plants, is only rarely used for phylogeny estimation in arthropods, although universal primers exist. This is partly due to difficulties in the alignment of ITS2 sequences in more distant taxa. The present study uses ITS2 secondary structure information to elucidate the phylogeny of a species-rich young radiation of arthropods, the butterfly subgenus Agrodiaetus. One aim is to evaluate the efficiency of ITS2 to resolve the phylogeny of the subgenus in comparison with COI , the most important mitochondrial marker in arthropods. Furthermore, we assess the use of compensatory base changes in ITS2 for the delimitation of species and discuss the prospects of ITS2 as a nuclear marker for barcoding studies.ResultsIn the butterfly family Lycaenidae, ITS2 secondary structure enabled us to successfully align sequences of different subtribes in Polyommatini and produce a Profile Neighbour Joining tree of this tribe, the resolution of which is comparable to phylogenetic trees obtained with COI+COII . The subgenus Agrodiaetus comprises 6 major clades which are in agreement with COI analyses. A dispersal-vicariance analysis (DIVA) traced the origin of most Agrodiaetus clades to separate biogeographical areas in the region encompassing Eastern Anatolia, Transcaucasia and Iran.ConclusionsWith the inclusion of secondary structure information, ITS2 appears to be a suitable nuclear marker to infer the phylogeny of young radiations, as well as more distantly related genera within a diverse arthropod family. Its phylogenetic signal is comparable to the mitochondrial marker COI . Compensatory base changes are very rare within Polyommatini and cannot be used for species delimitation. The implementation of secondary structure information into character-based phylogenetic methods is suggested to further improve the versatility of this marker in phylogenetic studies.

Project description:The genus Calisto Hübner, 1823 is the only member of the diverse, global subfamily Satyrinae found in the West Indies, and by far the richest endemic Caribbean butterfly radiation. Calisto species occupy an extremely diverse array of habitats, suggestive of adaptive radiation on the scale of other classic examples such as the Galápagos or Darwin's finches. However, a reliable species classification is a key requisite before further evolutionary or ecological research. An analysis of 111 DNA 'barcodes' (655 bp of the mitochondrial gene COI) from 29 putative Calisto species represented by 31 putative taxa was therefore conducted to elucidate taxonomic relationships among these often highly cryptic and confusing taxa. The sympatric, morphologically and ecologically similar taxa Calisto confusa Lathy, 1899 and Calisto confusa debarriera Clench, 1943 proved to be extremely divergent, and we therefore recognize Calisto debarriera stat. n. as a distinct species, with Calisto neiba Schwartz & Gali, 1984 as a junior synonym syn. n. Species status of certain allopatric, morphologically similar sister species has been confirmed: Calisto hysius (Godart, 1824) (including its subspecies Calisto hysius aleucosticha Correa et Schwartz, 1986, stat. n.), and its former subspecies Calisto batesi Michener, 1943 showed a high degree of divergence (above 6%) and should be considered separate species. Calisto lyceius Bates, 1935/Calisto crypta Gali, 1985/Calisto franciscoi Gali, 1985 complex, also showed a high degree of divergence (above 6%), confirming the species status of these taxa. In contrast, our data suggest that the Calisto grannus Bates, 1939 species complex (including Calisto grannus dilemma González, 1987, Calisto grannus amazona González, 1987, stat. n., Calisto grannus micrommata Schwartz & Gali, 1984, stat. n., Calisto grannus dystacta González, 1987, stat. n., Calisto grannus phoinix González, 1987, stat. n., Calisto grannus sommeri Schwartz & Gali, 1984, stat. n., and Calisto grannus micheneri Clench, 1944, stat. n.) should be treated as a single polytypic species, as genetic divergence among sampled populations representing these taxa is low (and stable morphological apomorphies are absent). A widely-distributed pest of sugar cane, Calisto pulchella Lathy, 1899 showed higher diversification among isolated populations (3.5%) than expected, hence supporting former separation of this species into two taxa (pulchella and darlingtoni Clench, 1943), of which the latter might prove to be a separate species rather than subspecies. The taxonomic revisions presented here result in Calisto now containing 34 species and 17 subspecies. Three species endemic to islands other than Hispaniola appear to be derived lineages of various Hispaniolan clades, indicating ancient dispersal events from Hispaniola to Puerto Rico, Cuba, and Jamaica. Overall, the degree of intrageneric and intraspecific divergence within Calisto suggests a long and continuous diversification period of 4-8 Myr. The maximum divergence within the genus (ca. 13.3%) is almost equivalent to the maximum divergence of Calisto from the distant pronophiline relative Auca Hayward, 1953 from the southern Andes (14.1%) and from the presumed closest relative Eretris Thieme, 1905 (14.4%), suggesting that the genus began to diversify soon after its split from its continental sister taxon. In general, this 'barcode' divergence corresponds to the high degree of morphological and ecological variation found among major lineages within the genus.

Project description:BackgroundNon-long terminal repeat (non-LTR) retrotransposons are mobile genetic elements that propagate themselves by reverse transcription of an RNA intermediate. Non-LTR retrotransposons are known to evolve mainly via vertical transmission and random loss. Horizontal transmission is believed to be a very rare event in non-LTR retrotransposons. Our knowledge of distribution and diversity of insect non-LTR retrotransposons is limited to a few species - mainly model organisms such as dipteran genera Drosophila, Anopheles, and Aedes. However, diversity of non-LTR retroelements in arthropods seems to be much richer. The present study extends the analysis of non-LTR retroelements to CR1 clade from four butterfly species of genus Maculinea (Lepidoptera: Lycaenidae).The lycaenid genus Maculinea, the object of interest for evolutionary biologists and also a model group for European biodiversity studies, possesses a unique, specialized myrmecophilous lifestyle at larval stage. Their caterpillars, after three weeks of phytophagous life on specific food plants drop to the ground where they are adopted to the ant nest by Myrmica foraging workers.ResultsWe found that the genome of Maculinea butterflies contains multiple CR1 lineages of non-LTR retrotransposons, including those from MacCR1A, MacCR1B and T1Q families. A comparative analysis of RT nucleotide sequences demonstrated an extremely high similarity among elements both in interspecific and intraspecific comparisons. CR1A-like elements were found only in family Lycaenidae. In contrast, MacCR1B lineage clones were extremely similar to CR1B non-LTR retrotransposons from Bombycidae moths: silkworm Bombyx mori and Oberthueria caeca.ConclusionThe degree of coding sequence similarity of the studied elements, their discontinuous distribution, and results of divergence-versus-age analysis make it highly unlikely that these sequences diverged at the same time as their host taxa. The only reasonable alternative explanation is horizontal transfer. In addition, phylogenetic markers for population analysis of Maculinea could be developed based on the described non-LTR retrotransposons.

Dataset Information

Does the DNA barcoding gap exist? - a case study in blue butterflies (Lepidoptera: Lycaenidae).

Publications

Does the DNA barcoding gap exist? - a case study in blue butterflies (Lepidoptera: Lycaenidae).

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