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Biogeography and systematics of Aricia butterflies (Lepidoptera, Lycaenidae)
Supplementary resource (1)
Data
September 2013
... To shed some light on the complexity of infection by Wolbachia in Polyommatinae, we studied two systems of closely related blue butterflies, the widely distributed Palaearctic genera Aricia Reichenbach, 1817, and Pseudophilotes Beuret, 1958. The taxonomy of these systems relies on often subtle differences in morphology, mitochondrial DNA data, life histories, or habitat diversification [26][27][28][29][30] . The few nuclear markers classically used in butterfly phylogeny often fail to distinguish these species 28,29 . ...
... The taxonomy of these systems relies on often subtle differences in morphology, mitochondrial DNA data, life histories, or habitat diversification [26][27][28][29][30] . The few nuclear markers classically used in butterfly phylogeny often fail to distinguish these species 28,29 . We focused on the taxa co-existing in Central Europe: Aricia agestis (Denis & Schiffermüller, 1775) and A. artaxerxes (Fabricius, 1793), as well as Pseudophilotes baton (Bergsträsser, 1779) and P. vicrama (Moore, 1865), and, for the latter genus, their closest relatives from other areas (i.e. the Pseudophilotes baton species complex). ...
... Aricia agestis and A. artaxerxes are believed to represent well-defined species. In the COI barcode, there is a constant minimum p-distance of about 2% between them, sufficient to distinguish two species 26,28 . They are not distinguished by some nuclear markers (e.g. ...
The bacterium Wolbachia infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of Wolbachia infection and mitochondrial diversity in two systems: Aricia agestis/Aricia artaxerxes and the Pseudophilotes baton species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two Wolbachia genes. Both butterfly systems had uninfected and infected populations, and harboured several Wolbachia strains. Wolbachia was highly prevalent in A. artaxerxes and the host's mitochondrial structure was shallow, in contrast to A. agestis. Similar bacterial alleles infected both Aricia species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the P. baton species complex mirrored its Wolbachia infection and not the taxonomical division. Pseudophilotes baton and P. vicrama formed a hybrid zone in Europe. Wolbachia could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for Wolbachia should be routine in mitochondrial DNA studies.
... Aricia agestis and A. artaxerxes, which are sympatric in Central Europe, differ in larval and pupal morphology, and rearing was traditionally used to distinguish them (Kames 1976;Lepidopterologen-Arbeitsgruppe 1987;Warecki 2010). Several studies combining morphology and molecular markers (Aagaard et al. 2002;Dincă et al. 2011;Sañudo-Restrepo et al. 2013) concluded that these taxa indeed represent true species and can be distinguished by allozyme profiles or the cytochrome c oxidase subunit 1 (COI, i.e., the standard DNA barcode for animals), but not by wing pattern or genital morphology. More specifically, adults from Scotland (nominotypical A. artaxerxes artaxerxes Fabricius, 1793) usually bear a white discoidal dot on the upper side of each brown fore wing. ...
... Ecologically and biogeographically, the majority of A. artaxerxes records appear concentrated in calcareous short-turf grasslands at high latitudes or elevations (Lepidopterologen-Arbeitsgruppe 1987;Asher et al. 2001;Aagaard et al. 2002;Sañudo-Restrepo et al. 2013;Pecsenye et al. 2014), where the species has a single annual generation from June to August. Its confirmed larval host plants across the range include Helianthemum Mill. ...
... In the wider geographical context, the overall COI genetic diversity within A. artaxerxes is low when compared to its sibling A. agestis (Sañudo-Restrepo et al. 2013;Vodă et al. 2015). ...
We report here the first molecular evidence for the occurrence of Aricia artaxerxes (Fabricius, 1793) (Lepidoptera: Lycaenidae) in the Czech Republic. In Central Europe, this species may co-occur with its more common sibling, Aricia agestis (Denis & Schiffermüller, 1775). We sequenced the cytochrome c oxidase subunit 1 of darkly-coloured, putative A. artaxerxes specimens in the Czech Republic. We confirmed A. artaxerxes only from a limestone area in South Bohemia (Vyšenské kopce National Nature Reserve), which is probably the only locality of the species in the Czech Republic. This area is located at ca. 550 m A.S.L., showing that the elevation overlap with A. agestis could be high in Central Europe. Other surveyed individuals were confirmed as A. agestis , with a minimum p-distance of 1.98% between the two species. The South Bohemian area of occurrence is probably highly isolated (approx. 190 km) from localities of the species in neighbouring countries, highlighting the conservation importance of the A. artaxerxes population and of the insular calcareous areas in the Šumava Mountains foothills. We used database sequences of A. artaxerxes to place the Czech population into a wider phylogeographic context. The Czech population is monomorphic, consisting of a single haplotype, which is present from Scandinavia through Germany to Central Asia.
... Among these, several examples of non-sister cryptic taxa with chequered distributions have been reported. Interestingly, such ecologically and morphologically similar species tend to be parapatric on mainland and apparently many display chequered distributions on islands, even over narrow sea straits [20][21][22][23][24][25]. Such a pattern could represent a signal of interspecific interactions [17,26,27]. ...
... cramera. The genetic structure and evolutionary relationships of these species have been recently documented [21,22]. Polyommatus icarus and P. celina are parapatric, habitat generalist species, are found over a broad altitudinal range, and feed on a wide array of host plants (Fig. 1A). ...
... Similarly, A. agestis is a habitat generalist and ubiquitous Palaearctic species that is phylogenetically closer to the boreo-montane A. artaxerxes and the montane A. montensis. The sister of this clade is A. cramera, which occurs in the south-western Mediterranean and is almost identical to A. agestis in ecology and external morphology, but it is differentiated genetically and in the male genital morphology [22] (Fig. 1B). The recognition of these taxa as species or subspecies has been debated [29,30], but what it is important in our case is that the phylogenetically divergent pairs are parapatric and show higher morphological similarity than the sympatric and phylogenetic closer taxa. ...
As cryptic diversity is being discovered, mostly thanks to advances in molecular techniques, it is becoming evident that many of these taxa display parapatric distributions in mainland and that they rarely coexist on islands. Genetic landscapes, haplotype networks and ecological niche modeling analyses were performed for two pairs of non-sister cryptic butterfly species, Aricia agestis-A. cramera and Polyommatus icarus-P. celina (Lycaenidae), to specifically assess non-coexistence on western Mediterranean islands, and to test potential causes producing such chequered distribution patterns. We show that the morphologically and ecologically equivalent pairs of species do not coexist on any of the studied islands, although nearly all islands are colonized by one of them. According to our models, the cryptic pairs displayed marked climatic preferences and 'precipitation during the driest quarter' was recovered as the most important climatic determinant. However, neither dispersal capacity, nor climatic or ecological factors fully explain the observed distributions across particular sea straits, and the existence of species interactions resulting in mutual exclusion is suggested as a necessary hypothesis. Given that the studied species are habitat generalists, feeding on virtually unlimited resources, we propose that reproductive interference, together with climatic preferences, sustain density-dependent mechanisms like "founder takes all" and impede coexistence on islands. Chequered distributions among cryptic taxa, both sister and non-sister, are common in butterflies, suggesting that the phenomenon revealed here could be important in determining biodiversity patterns.
... However, a recent study by Talavera et al. (2013) sug ges ted that P. c. nufrellensis might be more closely re lat ed to mainland populations of P. coridon than to P. c. gennargenti from the neighbouring island of Sar di nia. Therefore we carried out experimental hy bri di sa tion experiments between P. c. nufrellensis and a po pu la tion of the nominotypical subspecies from Ger ma ny. ...
... P. c. gen nargenti is more strongly differentiated from other po pulations of P. coridon and not especially closely re lated to P. c. nufrellensis. Talavera et al. (2013) dif fe ren tiated a western and an eastern clade within the co ri dongroup of taxa, with gennargenti in the former and nu frellensis in the latter clade. However, the bootstrap va lues for these two clades were low. ...
... Our network ana ly ses do not corroborate the existence of these two cla des, or the attribution of P. c. nufrellensis and P. c. gen nar genti to distinct clades. Instead, the westeast dif fe ren tiation is gradual, and our much increased data set shows many exceptions, one of which (a sequence of P. c. asturiensis from NW Spain in the eastern clade) was al ready noted by Talavera et al. (2013). The cline ap pears to be mainly the result of differential intro gres sion in the western and eastern part of the range. ...
In order to clarify the species status of the Corsican endemic Polyommatus (Lysandra) coridon nufrellensis we carried out experimental hybridisations with the nominotypical subspecies from Germany, because these can be informative about the existence of reproductive isolating mechanisms. Additionally, molecular analyses were done to resolve the degree of differentiation between both taxa. Six nufrellensis females could be mated to males of the nominotypical subspecies with the semi-artificial method. These
produced males and females of the F1 hybrid generation. One mating could be achieved amongst these hybrid butterflies. This mated female laid a very large number of eggs (433), most of which turned out to be fertile and produced 24 males and 19 females of the F2 generation. Adults of both the F1 and the F2 generation had characters of both parental taxa. An analysis of DNA sequences from the mitochondrial
(COI) as well as the nuclear genome (ITS2) with statistical parsimony networks did not provide evidence
for genetic differentiation of nufrellensis from the nominotypical subspecies. Our results point to a young and incomplete speciation process, and therefore we suggest keeping the current taxonomic treatment of nufrellensis as a subspecies of P. coridon. As an addendum to part II of our series on the coridon populations of the islands of Sardinia and Corsica we report the successful breeding of the F1 hybrid generation of P. c. gennargenti × P. c. nufrellensis to the F2 generation.
... In fact, most cryptic sister species occurring in Europe show a divergence time similar to that reported for Z. polyxena and Z. cassandra. However, no instances have been reported of both a strong diversification in genitalic structure and complete absence of introgression, as shown in our study [13], [16], [29], [49]. An important factor determining the evolution of two very distinct morphologies and genetic units is probably due to the low dispersal ability of Zerynthia
[54]. ...
... These studies also showed that most taxa hybridize at their contact areas. Hybrid zones are generally large (50–250 km) in butterfly species for which introgression occurs over their European range [13], [29], [49], [50], [51]. The cryptic butterflies Polyommatus icarus/P. ...
... cramera, for instance, have hybrid zones 200 and 50 km wide, respectively, and show clear phylogenetic divergence from 3% to 5% of COI sequences. Nevertheless, they show clear evidence of introgression with intermediate morphotypes and discrepancy between nuclear and mitochondrial DNA sequences [49], [52]. We sampled very close populations of Z. cassandra and Z. polyxena (Vercelli, Vigevano and Alessandria) with no apparent geographical barriers and analyzed specimens from the only area where the two species have been found in sympatry (Mount Beigua). ...
There is increasing evidence that most parapatric cryptic/sister taxa are reproductively compatible across their areas of contact. Consequently, the biological species concept, which assumes absence of interbreeding, is becoming a not so effective criterion in evolutionary ecology. Nevertheless, the few parapatric sister taxa showing complete reproductive barriers represent interesting models to study speciation processes and the evolution of reproductive isolation. In this study, we examined contact populations in northwestern Italy of two butterfly species, Zerynthia polyxena and Z. cassandra, characterized by different genitalic morphotypes. We studied levels of divergence among 21 populations distributed from Sicily to France using three genetic markers (the mitochondrial COI and ND1 genes and the nuclear wingless gene) and genitalic geometric morphometrics. Moreover, we performed species distribution modelling to estimate different climatic requirements of Z. polyxena and Z. cassandra. We projected climatic data into glacial maximum scenarios in order to verify if and to which extent glacial cycles could have contributed to speciation processes. Genetic and morphometric analyses identified two main groups. All specimens showed a concordant pattern of diversification, including those individuals sampled in the contact area. Haplotype distribution and climatic models showed that during glacial maxima both species experienced a strong range contraction and presumably remained separated into different microrefugia in southern France, in the Italian Peninsula and on the islands of Elba and Sicily. Long term separation was probably favoured by reduced dispersal ability and high phylopatry, while genitalic diversification probably favoured interbreeding avoidance. Conversely, the aposematic wing pattern remained almost identical. We compared our results with those obtained in other species and concluded that Z. polyxena and Z. cassandra represent a valuable model in the study of speciation.
... The Bootstrap and Jackknife indexes (based on a minimum of 10,000 replicates) were calculated as measures of branch support (Efron 1979;Miller 1974). The working phylogenetic hypothesis used for character optimization represents a consensus from different recent contributions to the phylogeny of Palaearctic Lycaenidae by Als et al. (2004), Kandul et al. (2004), Fric et al. (2007), Wiemers et al. (2009), andWiemers et al. (2010), with the relationships between the Tribe Polyommatini updated after the recent contributions by Sañudo-Restrepo et al. (2012) and Talavera et al. (2013). The basal position of Lycaena and a few other details follow Carnicer et al. (2013). ...
... Much of the recent work on the phylogenetics of this and other butterfly families (namely based on molecular evidence, e.g. Sañudo-Restrepo et al. 2012;Talavera et al. 2013 to mention two examples already quoted in this study) will lead to a necessary arrangement of the formally named supra-specific taxa, where the availability of diagnostic macroscopic features may become an urgent necessity. Consistent monophyletic entities that cannot be diagnosed on the basis of morphology are already known among the lycaenid butterflies (Talavera et al. 2013). ...
A morphological study with the use of scanning electron microscope of 67 species of Iberian Lycaenidae is presented. The study covers all the genera present in the area and shows an extraordinary variation in chorionic characters that allows egg diagnosis for most species. A morphometric study showed that the eggs from the sample have sizes that are correlated with adult size, but some species showed larger egg size than expected. Species hibernating at the egg stage proved to have on average larger sizes than those overwintering at other stages, probably because this trait might be favourable to endure the adverse conditions taking place during the winter. A cladistic analysis was performed using morphologic and morphometric characters from the egg with the result of poor discriminant power. However, some formal taxonomic groups such as the genera Lycaena and Satyrium were supported by our analysis due to specific apomorphic characters.
(This is the light version of the original study).
... to reproductively interfere between them (Pigot and Tobias 2013). Results for a series of cryptic butterfly species revealed only restricted contact zones on mainland and chequered distributions over narrow (3-10 km) sea straits (Dincă et al. 2011, Sañudo-Restrepo et al. 2013). If chequered distributions are overrepresented among cryptic species, they could encompass a disproportionally high fraction of beta-diversity turnover, a direct measure of the frequency of species replacement from site to site. ...
... This result could be explained if we assume that cryptic groups are composed by entities that recently evolved in allopatry and maintained their distribution pattern simply because they did not have enough time to disperse. However, many cryptic taxa in our study are not sister species and show substantial genetic divergence, while other morphologically differentiated species are their sister taxa; in most such cases a chequered distribution still occurs (Dincă et al. 2011, Sañudo-Restrepo et al. 2013). ...
The cryptic fraction of biodiversity is composed of morphologically similar species that are or have been overlooked by scientists. Although current research is increasingly documenting new cases, cryptic species are frequently ignored in large-scale studies and monitoring programs, either because they have not yet been discovered, or because of the practical difficulties involved in differentiating them. However, it is unknown if this could represent a bias extending beyond the number of missed species. By analyzing the butterfly fauna of the west Mediterranean (335 species), we defined cryptic spe- cies based on the current consensus of the scientific community, compared their properties to other congeneric species and investigated the consequences of their inclusion/exclusion in beta-diversity analyses. We show that, as defined, the cryptic fraction of butterfly diversity represents about 25% of the west Mediterranean fauna and is overwhelmingly composed by groups of species that are not sympatric. Our results show that co-occurrence among cryptic species is significantly lower than among congeneric non-cryptic species. Accordingly, albeit the frequency of cryptic species is homogenously distributed over the study area, their distribution pattern accounts for most beta-diversity turnover over sea (from 50 to 100%). Beta-diversity turnover, a direct measure of the frequency of species replacement from site to site, is recognized as a fundamental parameter in ecology and is widely used to detect biogeographic patterns. These findings represent a change of paradigm in showing that cryptic diversity comprises original qualitative aspects in addition to merely quantitative ones. This highlights the importance of differentiating cryptic species for various research fields and opens the door to the study of further potential particularities of cryptic diversity.
... A. montensis and A. cramera, also related and hardly distinguishable by external morphology, occur in the Iberian Peninsula, North Africa and, in the case of the latter, in the Balearic Islands and Sardinia. Aricia agestis has a parapatric distribution with all these taxa, and hybrids seem to occur at the contact zones (Sañudo-Restrepo et al., 2013;Vodă et al., 2015). ...
We present genome assemblies from two male Aricia agestis specimens (the Brown Argus; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequences are 435.3 and 437.4 megabases in span. Each assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genomes were assembled and are 15.47 and 15.45 kilobases in length. Gene annotation of these assemblies on Ensembl identified 12,688 and 12,654 protein coding genes.
... Melitaea cinxia and Aricia spp. butterflies also broadly comply to this biogeographic pattern and suture zone (Wahlberg & Saccheri 2007;Sañudo-Restrepo et al. 2013). The phenotypic and genetic independence of NW Iberian L. tityrus respective to Eastern Iberian and other European populations are further supported by long-term local habitat suitability spanning both glacials and interglacials (Fig. 7), and the AMOVA/ F ST analyses, which preferentially groups eastern Iberian populations among populations outside the Peninsula (Table 2, S4). ...
The comparison of closely related taxa is cornerstone in biology, as understanding mechanisms leading up to differentiation in relation to extant shared characters are powerful tools in interpreting the evolutionary process. Hotspots of biodiversity such as the west-Mediterranean, where many lineages meet are ideal grounds to study these processes. We set to explore the interesting example of Sooty Copper butterflies: widespread Eurasian Lycaena tityrus (Poda, 1761) comes into contact in Iberia with closely related and local endemic, L. bleusei (Oberthür, 1884), which hasn’t always been considered a distinct species. An integrative analysis was designed, combining the use of extensive molecular data (five genes), geometric morphometrics analyses, verified and up-to-date distribution data, and environmental niche modelling, aimed at deciphering their true relationship, their placement within European Lycaena and trace their evolutionary history. We revealed several levels of differentiation: L. bleusei and L. tityrus appear to be reciprocally monophyletic independent gene-pools, distinct in all genes analysed, having mutually diverged 4.8 Ma ago. L. tityrus but not L. bleusei, further displays a genetic structure compatible with several glacial refugia, where populations assignable to infraspecific taxa surface. Conversely, L. bleusei shows a loss in mtDNA diversity in relation to nuDNA. Morphological analyses differentiate both species according to size and shape but also discriminate strong seasonal and sexual traits and a geographical phenotype segregation in L. tityrus. Finally, updated distribution and its modelling for current and glacial timeframes reveal both species respond differently to environmental variables, defining a mostly parapatric distribution and an overlapping belt where sympatry was recovered. During the last glacial maximum, a wider expansion in L. bleusei distribution explains current isolated populations. Our study highlights the importance of gathering several lines of evidence when deciphering the relationships between closely related populations in the fringe of cryptic species realm.
... Enfin, certaines espèces ne sont déterminables avec certitude qu'avec la génétique. C'est le cas d'Aricia montensis Verity, 1928(SAÑUDO et al., 2013. Ces espèces ont été placées dans la catégorie « DD » et seules des études spécifiques pourront préciser leur répartition en Occitanie. ...
... Two methods of carrying out an extensive morphological study are, with traditional morphometry and geometric morphometry. In traditional morphometry, linear measurements made directly on the voucher specimen (Gillespie et al., 2013) or on a digital photograph (Hill et al., 2013;Sañudo-Restrepo et al., 2013) are used for multivariate statistical analyses. Geometric morphometry quantifies shape in 2D and 3D space with measurements taken on digital photographs with the use of stereomicroscopy and specialised software packages (Dincă et al., 2011a;Habel et al., 2012). ...
Morphological variability among four species of Mycalesis in Sri Lanka that are difficult to discriminate due to their morphological similarity was investigated to identify characters that distinguish species more accurately. Using traditional morphometrics, 90 variables from the wing, forelegs and genitalia of M. perseus typhlus, M. mineus polydecta, M. subdita and M. rama were measured and analysed. A set of 19 characters of the wing, male genitalia and forelegs were identified to discriminate species. Results of the analysis showed that male specimens were discriminated with nine wing characters and five characters of genitalia. Females could be discriminated with three wing characters and two foreleg characters. Male specimens of M. p. typhlus and M. m. polydecta showed the greatest morphological differentiation, while females of M. subdita and M. rama were the most similar species. These results were used to improve the currently available identification key. Two instances of possible hybridisation were discovered: one between M. p. typhlus and M. m. polydecta and the other between M. p. typhlus and M. subdita. Hence, the species of Mycalesis, particularly M. p. typhlus, M. m. polydecta and M. subdita may not be strictly reproductively isolated in Sri Lanka. Preliminary comparisons of M. p. typhlus in Sri Lanka with M. p. tabitha of India indicated that the Sri Lankan subspecies is unlikely to be a synonym.
... In Sardinia, A. agestis is replaced by the South-Western taxon A. cramera. The two taxa show a rather low COI divergence (around 2.4% depending on different haplotypes) (Sañudo-Restrepo et al., 2013). For this reason, A. agestis from Tuscany, Tuscan islands and Corsica and A. cramera from Sardinia have been used together in the analyses. ...
... Despite current progress in studies of blue butterflies belonging to the subtribe Polyommatina (e.g. LUKHTANOV et al. 2008LUKHTANOV et al. , 2014LUKHTANOV et al. , 2015VODO-LAZHSKY & STRADOMSKY 2010;WIEMERS et al. 2010;TALAVERA et al. 2013aTALAVERA et al. , 2013bSANUDO-RESTREPO et al. 2013;PRZYBY£OWICZ et al. 2014;STRADOMSKY 2014;SHAPOVAL & LUKHTANOV 2015a, 2015bECKWEILER & BOZANO 2016), a large number of unresolved taxonomic problems still persist in this group. Among them, the taxonomic position of the enigmatic species Polyommatus avinovi Stshetkin, 1980 is one of the most challenging questions. ...
Polyommatus avinovi (Stshetkin, 1980), an enigmatic taxon from Tajikistan has been considered in the literature either as a member of the genus Polyommatus, or a taxon belonging to the genus Rimisia. None of the conclusions on taxonomy and nomenclature of P. avinovi were supported by molecular or cytological data, therefore the problem of identity and phylogenetic position of this taxon has remained unsolved. Here we use the barcoding fragment of the COI gene as a molecular marker to demonstrate that none of these hypotheses are true. Phylogenetic analysis revealed P. avinovi to be strongly differentiated from both Polyommatus and Rimisia. Instead, it formed a separated, well supported monophyletic clade within the genus Afarsia Korb & Bolshakov, 2011. Thus, we propose the following new combinations for this butterfly: Afarsia avinovi comb. nov. and Afarsia avinovi dangara comb. nov.
... Higgins & Riley, 1970;Tolman & Lewington, 2008;Tshikolovets, 2011), but also as a distinct species, based on crossing experiments and on differences in the morphology of the genitalia (Higgins, 1975;Balletto et al., 1981;Kudrna et al., 2011). Recent molecular data support the species status of the two taxa (Sañudo-Restrepo et al., 2013;Vodă et al., 2015), but in this study we treated them as a group since they show a minimum COI p-distance lower than 3%. Aricia agestis and A. cramera are parapatric, with a contact zone in northeastern Iberian Peninsula, and they have never been found in sympatry on any Mediterranean island. ...
... In addition to creating a tool for DNA-based specimen identification, the Iberian dataset coupled with GMYC analysis permitted the first large-scale assessment of genetic patterns and potential cryptic diversity in European butterflies. Although European butterflies are among the best-studied invertebrate groups and considerable efforts have been devoted towards revealing hidden diversity, recent studies continue to report new cryptic species [41][42][43][44] . Conversely, some previously accepted species have been shown not to deserve their taxonomic status 45 . ...
How common are cryptic species-those overlooked because of their morphological similarity? Despite its wide-ranging implications for biology and conservation, the answer remains open to debate. Butterflies constitute the best-studied invertebrates, playing a similar role as birds do in providing models for vertebrate biology. An accurate assessment of cryptic diversity in this emblematic group requires meticulous case-by-case assessments, but a preview to highlight cases of particular interest will help to direct future studies. We present a survey of mitochondrial genetic diversity for the butterfly fauna of the Iberian Peninsula with unprecedented resolution (3502 DNA barcodes for all 228 species), creating a reliable system for DNA-based identification and for the detection of overlooked diversity. After compiling available data for European butterflies (5782 sequences, 299 species), we applied the Generalized Mixed Yule-Coalescent model to explore potential cryptic diversity at a continental scale. The results indicate that 27.7% of these species include from two to four evolutionary significant units (ESUs), suggesting that cryptic biodiversity may be higher than expected for one of the best-studied invertebrate groups and regions. The ESUs represent important units for conservation, models for studies of evolutionary and speciation processes, and sentinels for future research to unveil hidden diversity.
... Higgins 1975 on the European species; Scott & Wright 1990 who included the North-American taxa). Thus in spite of the availability of a number of characters of potential taxonomic interest (such as those on the adult genitalia used by Higgins 1975) no cladistic reanalysis of the whole taxon has been attempted, as the recent phylogenetic work in this family has concentrated on selected low-rank subtaxa Megens et al. 2004Megens et al. , 2005Pratt et al. 2006Pratt et al. , 2011Robbins et al. 2010;Wiemers et al. 2010;Ugelvig et al. 2011;Sañudo-Restrepo et al. 2013;Talavera et al. 2013). ...
We test the extent to which the combination of 69 morphological characters from the early stages (18 from the egg, six larval and eight pupal) with 37 adult morphological characters of the lycaenids (Lepidoptera: Lycaenidae) improves the results of a parsimony analysis to reconstruct the evolutionary history of the group, using 51 sample species from the West Palaearctic. The results show three main clades, although with low support from bootstrap and jackknife resamplings; they represent the four tribes present in our sample, i.e. Lycaenini, Theclini, Eumaeini and Polyommatini. The tribe Lycaenini (the one that has the highest node support) is in the base of the tree. Theclini + Eumaeini appear as sister clades with the Polyommatini as the sister taxon to both of them. At the lowest taxonomic levels our results are often in agreement with those from recent studies done on a molecular basis. Adding morphological information from the immature stages to that of the adult contributed significantly to increasing the resolution of the resulting cladogram. Our results confirm the idea that combined data matrices (e.g. including information from different life stages) may generally result in more consistent phylogenetic trees than those based in the adult morphology alone.
... Whereas endemism tends to be generally low and mostly concentrated in the Sardo-Corsican area, there are several species that have higher incidence on islands than on the nearest mainland (e.g. Pontia daplidice, Polyommatus celina, Aricia cramera, Argynnis pandora, Coenonympha lyllus and several Hipparchia taxa), probably representing relict occurrences from past wider distributions (Dapporto & Dennis, 2008;Dinc a et al., 2011;Dapporto et al., 2012;Sañudo-Restrepo et al., 2013). As a result, these distributions produce an aggregation of islands in the b sor analyses, reducing their similarity with respect to the mainland source sites. ...
Aim
Unpartitioned dissimilarity indices such as the Sørensen index (β sor ) tend to categorize areas according to species number. The use of turnover indices, such as the Simpson index (β simp ), may lead to the loss of important information represented by the nestedness component (β nest ). Recent studies have suggested the importance of integrating nestedness and turnover information. We evaluated this proposition by comparing biogeographical patterns obtained by unpartitioned (β sor ) and partitioned indices (β simp and β nest ) on presence data of western Mediterranean butterflies.
Location
Western Mediterranean.
Methods
We assessed the regionalization of 81 mainland and island faunas according to partitioned and unpartitioned dissimilarity by using cluster analyses with the unweighted pair‐group method using arithmetic averages ( UPGMA ) combined with non‐metric multidimensional scaling ( NMDS ). We also carried out dissimilarity interpolation for β sor , β simp , β nest and the β nest /β sor ratio, to identify geographical patterns of variation in faunal dissimilarity.
Results
When the unpartitioned β sor index was used, the clustering of sites allowed a clear distinction between insular and mainland species assemblages. Most islands were grouped together, irrespective of their mainland source, because of the dominant effect of their shared low richness. β simp was the most effective index for clustering islands with their respective mainland source. β simp clustered mainland sites into broader regions than clusters obtained using β sor . A comparison of regionalization and interpolation provided complementary information and revealed that, in different regions, the patterns highlighted by β sor could largely be determined either by nestedness or turnover.
Main conclusions
Partitioned and unpartitioned indices convey complementary information, and are able to reveal the influence of historical and ecological processes in structuring species assemblages. When the effect of nestedness is strong, the exclusive use of turnover indices can generate geographically coherent groupings, but can also result in the loss of important information. Indeed, various factors, such as colonization–extinction events, climatic parameters and the peninsular effect, may determine dissimilarity patterns expressed by the nestedness component.
... Tshikolovets 2011; Table 2). Aricia artaxerxes (Fabricius, 1793) and Aricia montensis Verity, 1928 are treated in CLIMBER as distinct species with parapatric distributions (see Sanudo-Restrepo et al. 2013). The latter species is confined to the Iberian Peninsula and North Africa. ...
Detailed information on species’ ecological niche characteristics that can be related to declines and extinctions is indispensable for a better understanding of the relationship between the occurrence and performance of wild species and their environment and, moreover, for an improved assessment of the impacts of global change. Knowledge on species characteristics such as habitat requirements is already available in the ecological literature for butterflies, but information about their climatic requirements is still lacking. Here we present a unique dataset on the climatic niche characteristics of 397 European butterflies representing 91% of the European species (see Appendix). These characteristics were obtained by combining detailed information on butterfly distributions in Europe (which also led to the ‘Distribution Atlas of Butterflies in Europe’) and the corresponding climatic conditions. The presented dataset comprises information for the position and breadth of the following climatic niche characteristics: mean annual temperature, range in annual temperature, growing degree days, annual precipitation sum, range in annual precipitation and soil water content. The climatic niche position is indicated by the median and mean value for each climate variable across a species’ range, accompanied by the 95% confidence interval for the mean and the number of grid cells used for calculations. Climatic niche breadth is indicated by the standard deviation and the minimum and maximum values for each climatic variable across a species’ range. Database compilation was based on high quality standards and the data are ready to use for a broad range of applications.
It is already evident that the information provided in this dataset is of great relevance for basic and applied ecology. Based on the species temperature index (STI, i.e. the mean temperature value per species), the community temperature index (CTI, i.e. the average STI value across the species in a community) was recently adopted as an indicator of climate change impact on biodiversity by the pan-European framework supporting the Convention on Biological Diversity (Streamlining European Biodiversity Indicators 2010) and has already been used in several scientific publications. The application potential of this database ranges from theoretical aspects such as assessments of past niche evolution or analyses of trait interdependencies to the very applied aspects of measuring, monitoring and projecting historical, ongoing and potential future responses to climate change using butterflies as an indicator.
1. The association of darker, less reflective insect wings with cooler environments (Bogert’s rule) is thought to be related to adult thermoregulation, but the adaptive explanation and the implications for sensitivity to climate warming are yet to be tested. We re-evaluate the pattern for butterflies using finer resolution data than in previous approaches, both geographically and morphologically, and test its correlation with recent evidence of impacts of warming on butterflies.
2. We compared reflectance–climate relationships at different grid sizes, selected the best subset of reflectance measurements and tested the contribution of the species basking mode, the phylogenetic structure of the data and the correlation between reflectance and published abundance or altitudinal shifts. We used standardised RGB (Red, Green, Blue) values from 222 species from the Iberian Peninsula, and regional mean temperature and precipitation data from the study area (10 and 50-km resolutions) and Europe (50-km resolution).
3. Correlations between reflectance and temperature increased at finer geographical and morphological resolutions. However, the butterfly basking mode did not improve the statistical explanation of the pattern. Reflectance shows a strong phylogenetic structure, while variance partitioning indicated a poor pure contribution of the climate variables in the reflectance–climate correlation.
4. Overall, mean temperature and precipitation were only modest predictors of butterfly reflectance. No correlation between reflectance and recent abundance or altitudinal shifts was found using the hypothesised best estimates of reflectance. Although significant correlations between butterfly shading and altitudinal shifts were found for two of the reflectance measurements, this is interpreted as weak, probably artifactual evidence on the predictive power of this relationship.
5. The strong phylogenetic pattern of the reflectance and the low fraction of the reflectance measures analysed suggest that tests for alternative explanations are still needed to shed light on the meaning of the colour–environment relationships in butterflies, which probably are of a complex nature. From an adaptive point of
view, unravelling the basis of Bogert’s pattern in butterflies requires a closer,abitat-level approach and alternative variables to adult thermoregulatory behaviour to be tested.
We present a genome assembly from an individual Aricia artaxerxes (the northern brown argus; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 458 megabases in span. Most of the assembly (99.99%) is scaffolded into 23 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,688 protein coding genes.
The Black-veined White Aporia crataegi (Linnaeus, 1758), a common and widespread butterfly ranging from northwestern Africa to Europe and Asia, has been extinct in Britain since the 1920s and is on a steady decline in several other parts of its range. In order to investigate genetic diversity within A. crataegi and its correspondence with current subspecies-level taxonomy, we barcoded 173 specimens from across its range including, for the first time, extinct populations from Britain and Korea. Using next generation sequencing we also obtained a sequence for Aporia joubini, a peculiar taxon from China known only by its type specimen collected in the early twentieth century. Our phylogenetic analysis placed A. joubini sister to A. oberthuri, although further taxon sampling may reveal a different scheme. Within A. crataegi, we observed a shallow and weak mitogenomic structure with only a few distinct lineages in North Africa, Sicily, Iran, and Japan. Eurasian populations, including those extinct in Britain and Korea, clustered into a large set of closely allied lineages, consistent with a recent expansion during the Late Pleistocene glacial period. This study highlights the importance of museum collections and the unique opportunities they provide in documenting species diversity and helping conservation efforts.
Background
There is a widely recognized need for more comprehensive understanding of patterns of global biodiversity. Such information will not only provide insights into major scientific issues, such as speciation mechanisms, but it will also add new rigor to conservation programs (a critical need given the looming extinction crisis). We exploit the power of DNA barcoding to explore biodiversity patterns in European butterflies, one of the best studied invertebrate groups in the world. Ongoing research allowed the detection of unexpected genetic patterns (exemplified here by Leptidea and Spialia), illustrating the biological complexity that awaits discovery even in exhaustively studied regions.
Results
The intensively studied model species-pair Leptidea sinapis and Leptidea reali has recently been shown to actually represent a triplet of species displaying genetic differences and reproductive isolation due to female mate choice. Additional research has shown that L. sinapis is currently the metazoan with the highest intraspecific chromosome number variability (2n=56 to 2n=110), unrelated to polyploidy, and that its chromosomal races seem to follow a longitudinally-oriented cline. This unique system prompted us to test the role of chromosomal rearrangements in speciation and the concept of clinal species by mating extreme chromosomal races based on laboratory lines of L. sinapis. Within the genus Spialia, recent research stimulated by DNA barcodes suggests the presence of a new cryptic species confined to Iberia that has likely speciated through larval host-plant shift. Complex patterns of Wolbachia infections have been detected in both Leptidea and Spialia.
Significance
Leptidea and Spialia represent some of the most striking cases of cryptic species in European butterflies. These taxa exemplify the effort that lies ahead when documenting biodiversity and show how patterns detected by DNA barcodes can lead to the discovery of exciting systems that can often act as models to improve our understanding of fundamental evolutionary processes.
The butterfly fauna of Russia is completely reviewed, with keys compiled for the 472 species in 140 genera occurring in the country. Surveys of their taxonomy and brief remarks on distribution and ecology are provided. The male genitalia and some other structures of all these taxa are depicted in more than 700 figures arranged in 41 plates, 472 distribution maps, and 119 colour photos of the butterflies in nature.
Transcontinental dispersals by organisms usually represent improbable events that constitute a major challenge for biogeographers. By integrating molecular phylogeny, historical biogeography and palaeoecology, we test a bold hypothesis proposed by Vladimir Nabokov regarding the origin of Neotropical Polyommatus blue butterflies, and show that Beringia has served as a biological corridor for the dispersal of these insects from Asia into the New World. We present a novel method to estimate ancestral temperature tolerances using distribution range limits of extant organisms, and find that climatic conditions in Beringia acted as a decisive filter in determining which taxa crossed into the New World during five separate invasions over the past 11 Myr. Our results reveal a marked effect of the Miocene–Pleistocene global cooling, and demonstrate that palaeoclimatic conditions left a strong signal on the ecology of present-day taxa in the New World. The phylogenetic conservatism in thermal tolerances that we have identified may permit the reconstruction of the palaeoecology of ancestral organisms, especially mobile taxa that can easily escape from hostile environments rather than adapt to them.
The generic composition of the Polyommatus Section of the Polyommatini, originally proposed by Eliot mostly from studies of male genitalia and including 33 valid generic names, is revised.
Recent revisionary works, including study of morphological (and other) characters in both sexes indicates the following genera must be excluded: Cyclargus Nabokov, 1945; Echinargus Nabokov, 1945; Hemiargus Hubner, [1819]; Itylos Draudt, 1921 (= Parachilades Nabokov, 1945); Nabokovia Hemming, 1960 and Pseudochrysops Nabokov, 1945.
Characters are reviewed for the nine genera remaining in Polyommatus Section:
Agriades Hubner, [1819];
AlbulinaTurr, 1909 (= Farsia Zhdanko, 1992, syn. nov.; Pamiria Zhdanko, 1994, syn. nov.; Patricius Balint, 1991, syn. nov. and Plebejidea Koqak, 1993, syn. nov.);
Aricia [Reichenbach], 1819 (= Umpria Zhdanko, 1994, syn. nov.);
Chilades Moore, [1881] (= Lachides Nekrutenko, 1984, syn. nov.);
Madeleinea Balint, 1993;
Paralycaeides Nabokov, 1945;
Plebejus Kluk, 1802 (= Alpherakya Zhdanko 1994, syn. nov.);
Polyommatus Latreille, 1804 (= Elviria Zhdanko, 1994, syn. nov.) and Pseudolucia Nabokov, 1945.
A list of genera and species is given. Three replacement names are proposed:
Plebejus ardis Balint & Johnson, nom. nov. (replaces Lycaena eversmanni Staudinger, 1894), Plebejus beani Balint & Johnson, nom. nov. (replaces Lycaena indica Evans, 1925) and Plebejus pilgram Balint & Johnson, nom. nov. (replaces Lycaena serica Grum-Grshimailo, 1902).
From examination of type material, the following new species level synonymies are established: Aricia monarchus Higgins, 1981 (junior synonym of Papilio semiargus Rottemburg, 1775), Lycaena idas tshimgana Forster, 1936 (junior synonym of Lycaena argus f. naruena Courvoisier, 1913),
Plebejus balinti D’Abrera, 1993 (junior synonym of Lycaena buddhista Alpheraky, 1881), Polyommatus tibetanus Forster, 1940 (junior synonym of Polyommatus annulatus Elwes, 1906) and Vacciniina lornex Higgins, 1981 (junior synonym of Plebejus lucifera selengensis Forster, 1940).
A hypothetical branching diagram of the Polyommatus Section is presented and discussed, with notes concerning historical context (especially regarding the Plebejinae system of Nabokov). The phenomenon of wing discoloration in certain Polyommatini is discussed in light of new data concerning geographic distribution and apparent endemism in various of these taxa. Also examined are historical and current methods of studying the Polyommatini and various views of the tribes’s overall diversity.
In an Appendix, six polyommatine lycaenids are described: Agriades kurtjohnsoniBAum. spec. nov. from Nepal, Albulina gaborronkayi Balint, spec. nov. also from Nepal, Polyommatus frauvartianae spec. nov. from Afghanistan, Polyommatus fabiani spec. nov. from Mongolia, Polyommatus delessei spec. nov. from Iran and Madeleinea gradoslamasi spec. nov. from Peru.
Lycaenid butterflies of the Aricia agestisartaxerxes complex pose an unresolved taxonomic and conservation problem in northwestern Europe. Two key issues require resolution: (i) how many species of Aricia occur in northwestern Europe and what are their distributions?; (ii) how is the morphological variation observed in northwestern Europe best explained? We investigated phylogenetic relationships and phylogeographic patterns in this species group using mitochondrial and nuclear markers in comparison with morphological variation. A 325 bp fragment of the mitochondrial cytochromeb gene was sequenced from 179 individuals representing 18 populations from the UK and Scandinavia. Seventeen enzymecoding loci were analysed from 538 individuals from the same populations. Highly congruent phylogenies between mitochondrial and allozyme markers demonstrate that the sample is composed of two closely related species, A. agestis and A. artaxerxes. Both marker types also suggest that Scottish and northern Scandinavian A. artaxerxes populations are conspecific, and consequently do not support the endemic status of A. artaxerxes in the UK. The subspecies division of British populations of A. artaxerxes is also not supported by phylogenetic analyses. Allozyme and mitochondrial analyses cluster two populations from the Peak District, UK, differently. The former suggests that they are A. artaxerxes whilst the latter suggests they are A. agestis. Further research is required to find the reason for this disagreement, which could be associated with the different dynamics of nuclear and mitochondrial genes across a hybrid zone between the two species. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 75, 27–37.
Progress in understanding the higher classification of butterflies has not kept pace with increase in the number of described species. Important points of uncertainty or contention include, apart from ranking problems, monophyly of Papilionoidea plus Hesperioidea, their relationship with other Lepidoptera in general and the Hedyloidea in particular, the question of the sister group of the Pieridae (either Papilionidae, or Lycaenidae + Nymphalidae), and the division of families into subfamilies. Traditional groupings are discussed and compared with the results of a cladistic analysis using 103 characters and 74 species (59 butterflies and 15 moths). The cladistic analysis supports a number of currently held views about butterfly classification, such as monophyly of five major family groupings (Hesperiidae, Papilionidae, Pieridae, Lycaenidae and Nymphalidae) and suggests sister group relationships between Papilionoidea and Hesperioidea, and Pieridae and (Lycaenidae + Nymphalidae). Most traditional subfamilies, however, are not supported on the basis of the data set used but the Riodininae, which always appeared as a monophyletic, subordinate group within the Lycaenidae, are a notable exception. Further, the analysis suggests that, contrary to traditional ideas, the Parnassiinae, not Baroniinae, are sister to the remainder of the Papilionidae, Pseudopontiinae are internal to (Pierinae + Coliadinae), Dismorphiinae are sister to all other Pieridae, and that Liptena, Poritia and Miletus represent the closest relatives of the Riodininae. The data set is not well suited for an assessment of the position of the butterflies amongst other Lepidoptera. Nevertheless, of the moths used, Macrosoma (Hedylidae, Hedyloidea) and Urania (Uraniidae, Geometroidea) appear to be the closest relatives of the butterflies. With regard to the higher classification of the butterflies many problems thus remain, and several ways to tackle these are discussed. The need for some form of international co-operation between fieldworkers, comparative morphologists and molecular systematists is stressed.
1. Distribution changes brought about by climate change are likely to alter levels of hybridisation between related taxa, and may threaten some species.
2. Nuclear (Tpi) and mitochondrial (cytB) DNA sequence data give evidence for introgression between two related Polyommatus (subgenus Aricia) butterfly species in a 150–200 km wide overlap zone in northern England and North Wales. A history of hybridisation is evident from the mixture of genotypes present within this region: some populations contain southern-origin (Polyommatus agestis) mtDNA and northern-origin (Polyommatus artaxerxes) Tpi alleles, and many populations contain mixtures of Tpi alleles.
3. The timing of the original hybridisation is unknown, but could be immediately post-glacial or much more recent in origin.
4. Both species are now beginning to shift northwards, associated with recent climatic warming.
5. It is thus expected that anthropogenic climate change will unleash a new spate of hybridisation, potentially threatening the long-term survival of the northern species in Britain.
DNA barcoding employs short, standardized gene regions (5' segment of mitochondrial cytochrome oxidase subunit I for animals) as an internal tag to enable species identification. Prior studies have indicated that it performs this task well, because interspecific variation at cytochrome oxidase subunit I is typically much greater than intraspecific variation. However, most previous studies have focused on local faunas only, and critics have suggested two reasons why barcoding should be less effective in species identification when the geographical coverage is expanded. They suggested that many recently diverged taxa will be excluded from local analyses because they are allopatric. Second, intraspecific variation may be seriously underestimated by local studies, because geographical variation in the barcode region is not considered. In this paper, we analyse how adding a geographical dimension affects barcode resolution, examining 353 butterfly species from Central Asia. Despite predictions, we found that geographically separated and recently diverged allopatric species did not show, on average, less sequence differentiation than recently diverged sympatric taxa. Although expanded geographical coverage did substantially increase intraspecific variation reducing the barcoding gap between species, this did not decrease species identification using neighbour-joining clustering. The inclusion of additional populations increased the number of paraphyletic entities, but did not impede species-level identification, because paraphyletic species were separated from their monophyletic relatives by substantial sequence divergence. Thus, this study demonstrates that DNA barcoding remains an effective identification tool even when taxa are sampled from a large geographical area.
DNA barcoding aims to accelerate species identification and discovery, but performance tests have shown marked differences in identification success. As a consequence, there remains a great need for comprehensive studies which objectively test the method in groups with a solid taxonomic framework. This study focuses on the 180 species of butterflies in Romania, accounting for about one third of the European butterfly fauna. This country includes five eco-regions, the highest of any in the European Union, and is a good representative for temperate areas. Morphology and DNA barcodes of more than 1300 specimens were carefully studied and compared. Our results indicate that 90 per cent of the species form barcode clusters allowing their reliable identification. The remaining cases involve nine closely related species pairs, some whose taxonomic status is controversial or that hybridize regularly. Interestingly, DNA barcoding was found to be the most effective identification tool, outperforming external morphology, and being slightly better than male genitalia. Romania is now the first country to have a comprehensive DNA barcode reference database for butterflies. Similar barcoding efforts based on comprehensive sampling of specific geographical regions can act as functional modules that will foster the early application of DNA barcoding while a global system is under development.
Current 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.
In 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.
With 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.
The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species
level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule
plays a vital role. We have developed the ITS2 Database (http://its2.bioapps.biozentrum.uni-wuerzburg.de) which holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank. In the new version,
we use Hidden Markov models (HMMs) for the identification and delineation of the ITS2 resulting in a major redesign of the
annotation pipeline. This allowed the identification of more than 160 000 correct full length and more than 50 000 partial
structures. In the web interface, these can now be searched with a modified BLAST considering both sequence and structure,
enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple
template structures. Sequences can be searched for known and newly identified motifs. Together, the database and the web server
build an exhaustive resource for ITS2 based phylogenetic analyses.
The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. There are several tools available that help performing these tasks, but all of them are specialized and focus on only one aspect, editing the alignment or plotting the secondary structure. The problem is both these tasks need to be performed simultaneously.
4SALE is designed to handle sequence and secondary structure information of RNAs synchronously. By including a complete new method of simultaneous visualization and editing RNA sequences and secondary structure information, 4SALE enables to improve and understand RNA sequence and secondary structure evolution much more easily.
4SALE is a step further for simultaneously handling RNA sequence and secondary structure information. It provides a complete new way of visual monitoring different structural aspects, while editing the alignment. The software is freely available and distributed from its website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de/
We describe "universal" DNA primers for polymerase chain reaction (PCR) amplification of a 710-bp fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) from 11 invertebrate phyla: Echinodermata, Mollusca, Annelida, Pogonophora, Arthropoda, Nemertinea, Echiura, Sipuncula, Platyhelminthes, Tardigrada, and Coelenterata, as well as the putative phylum Vestimentifera. Preliminary comparisons revealed that these COI primers generate informative sequences for phylogenetic analyses at the species and higher taxonomic levels.
The neotropical Heliconius butterflies are famous examples of Müllerian mimicry, due to the diverse array of shared, brightly colored wing patterns that advertise the butterflies' unpalatability. The parallel geographical variation in these patterns within several widespread species has been invoked to support the controversial Pleistocene refugium hypothesis of tropical diversification. However, in no Heliconius species have either evolutionary rates or relationships among geographical races been explicitly examined. I present a phylogenetic hypothesis based on mitochondrial DNA sequences for 14 divergent races of Heliconius erato, which reveals that similar wing patterns have evolved rapidly and convergently within the species. There is a basal split between groups of races from east and west of the Andes, reflecting a vicariant separation at the base of the Pleistocene. Within each of these clades, sequence divergence is very low, and some haplotypes are shared between allopatric races with radically different wing patterns. The topology implies a simultaneous radiation of races in these two areas within the last 200,000 years. Ages for the clades are estimated by comparing sequence divergence to a plot of mitochondrial divergence in several arthropod taxa with independently dated divergence times. This plot is linear and suggests that mitochondrial DNA in arthropods evolves in a clocklike manner, at least initially, when sequence divergence is low.
In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously.
4SALE fills this gap. The application allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis.
4SALE, which provides an user-friendly and intuitive interface, is a comprehensive toolbox for RNA analysis based on sequence and secondary structure information. The program connects sequence and structure databases like the ITS2 Database to phylogeny programs as for example the CBCAnalyzer. 4SALE is written in JAVA and therefore platform independent. The software is freely available and distributed from the website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de.
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.
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.
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.
The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented.
BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license.
BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.
jModelTest is a new program for the statistical selection of models of nucleotide substitution based on “Phyml” (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696–704.). It
implements 5 different selection strategies, including “hierarchical and dynamical likelihood ratio tests,” the “Akaike information
criterion,” the “Bayesian information criterion,” and a “decision-theoretic performance-based” approach. This program also
calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate
of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment
installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. C SIMON, F FRATI, A BECKENBACH, B CRESPI, H LIU, P
Observations during the breeding of Polyommatus (Aricia) torulensis (Lepidoptera: Lycaenidae) Between the years 1994 and 1996 the biotope of Polyommatus (Aricia) torulensis Hesselbarth & Siepe, 1993 in the Northeast of Turkey was visited three times, to get some facts about the ecology and biology of this blue. The eggs are deposited in the wild on the leaves of a Geranium species with violet flowers and bright leaves. The plant grows on steep west situated cliffs which are difficult accessible. Few eggs were obtained in captivity, from which 20% of the larvae hatched during late summer. From the remaining eggs the larvae hatched in spring. The rearing was less successful because of cannibalism, only 1 female and 1 male hatched, both of them were very large. The larva and pupa produce substrate-borne vibrations when disturbed. The larva possesses in the third and fourth instar a dorsal nectary organ on A7 and paired eversible tentacle organs on A8. Whether torulensis can be considered to be a separate species depends on the results of further studies within the Aricia group. Samenvatting.Waarnemingen tijdens de kweek van Polyommatus (Aricia) torulensis (Lepidoptera: Lycaenidae) In de tijdspanne 1994-1996 werd de biotoop van Polyommatus (Aricia) torulensis Hesselbarth & Siepe, 1993 in het noordoosten van Turkije driemaal bezocht om gegevens over de ecologie en de biologie van deze soort te verzamelen. De eieren worden in de natuur afgezet op de bladeren van een Geranium-soort met paarse bloemen en lichte bladeren. De plant groeit op steile, naar het westen gerichte en moeilijk toegankelijke hellingen. Enkele eieren werden in gevangenschap afgezet, waarvan 20% in de late zomer de rupsen leverden. De overige eieren kwamen uit in de lente. De kweek was weinig succesvol wegens kannibalisme, slechts 1 mannetje en 1 vrouwtje ontpopten, beide erg grote exemplaren. De rups en de pop maken geluid bij storing. De rups bezit in het derde en vierde larvestadium een dorsaal nectarorgaan op A7 en gepaarde, uitstulpbare tentakels op A8. Of torulensis als aparte soort moet worden beschouwd, hangt af van de resultaten van verder onderzoek binnen de Aricia groep. Résumé. Observations pendant un élevage de Polyommatus (Aricia) torulensis (Lepidoptera: Lycaenidae) Durant la période 1994-1996 le biotope de Polyommatus (Aricia) torulensis Hesselbarth & Siepe, 1993 dans le nord-est de la Turquie fut visité trois fois afin de collecter des informations sur l'écologie et la biologie de cette espèce. Dans la nature les œufs sont déposés sur les feuilles d'une espèce de Geranium violet à feuilles claires. La plante pousse sur des pentes raides, orientées vers l'ouest et difficilement accessibles. Quelques œufs furent déposés dans des conditions de laboratoire, et seulement 20% donnèrent des chenilles vers la fin de l'été, les autres pendant le printemps suivant. L'élevage n'eut pas beaucoup de succès à cause du cannibalisme.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Rapid evolution of genitalia is one of the most general patterns of morphological diversification in animals. Despite its generality, the causes of this evolutionary trend remain obscure. Several alternative hypotheses have been suggested to account for the evolution of genitalia (notably the lock-and-key, pleiotropism, and sexual selection hypotheses). Here, I argue that thorough intraspecific studies are the key to gaining insight into the patterns and processes of genitalic evolution. Critical assumptions and predictions that may be used to distinguish between the different hypotheses are identified and discussed. However, current knowledge of selection on genitalia, or even of the degree of phenotypic and genotypic variability of genital morphology, is highly limited, allowing only a very tentative assessment of the various hypotheses. In-depth single species studies of current patterns and processes of selection on genitalia are badly needed, and a single species research program is briefly outlined.
Peer Reviewed http://deepblue.lib.umich.edu/bitstream/2027.42/31361/1/0000273.pdf
Despite the fact that Bicyclus anynana has become an important model species for wing-pattern developmental biology and studies of phenotypic plasticity, little is known of the evolutionary history of the genus Bicyclus and the position of B. anynana. Understanding the evolution of development as well as the evolution of plasticity can be attempted in this species-rich genus that displays a large range of wing patterns with variable degrees of phenotypic responses to the environment. A context to guide extrapolations from population genetic studies within B. anynana to those between closely related species has been long overdue. A phylogeny of 54 of the 80 known Bicyclus species is presented based on the combined 3000-bp sequences of two mitochondrial genes, cytochrome oxidase I and II, and the nuclear gene, elongation factor 1α. A series of tree topologies, constructed either from the individual genes or from the combined data, using heuristic searches under a variety of weighting schemes were compared under the best maximum-likelihood models fitted for each gene separately. The most likely tree topology to have generated the three data sets was found to be a tree resulting from a combined MP analysis with equal weights. Most phylogenetic signal for the analysis comes from silent substitutions at the third position, and despite the faster rate of evolution and higher levels of homoplasy of the mitochondrial genes relative to the nuclear gene, the latter does not show substantially stronger support for basal clades. Finally, moving branches from the chosen tree topology to other positions on the tree so as to comply better with a previous morphological study did not significantly affect tree length.
The information that can be obtained from the secondary structure of the nuclear ribosomal internal transcribed spacer 2 (ITS2) is substantial, and yet many studies exploit this information inconsistently or inappropriately. This review introduces a remedy in the form of a flowchart where we detail the steps involved in estimating structure-based phylogenetic trees from ITS2 data. The pipeline described consists of the ITS2 Database, 4SALE, the CBCAnalyzer, and ProfDistS. Based on these tools, we describe how to utilize ITS2 sequence and secondary structure information together with an ITS2 specific scoring matrix and an ITS2 specific substitution model. The phylogenetic results thus obtained have been shown to be more reliable than approaches based on primary sequence data alone. Moreover, compensatory base changes (CBCs) in ITS2 sequence–structure pairs are identified as a possible marker for distinguishing species.
In Butterflies: Ecology and Evolution Taking Flight, the world's leading experts synthesize current knowledge of butterflies to show how the study of these fascinating creatures as model systems can lead to deeper understanding of ecological and evolutionary patterns and processes in general. The twenty-six chapters are organized into broad functional areas, covering the uses of butterflies in the study of behavior, ecology, genetics and evolution, systematics, and conservation biology. Especially in the context of the current biodiversity crisis, this book shows how results found with butterflies can help us understand large, rapid changes in the world we share with themâfor example, geographic distributions of some butterflies have begun to shift in response to global warming, giving early evidence of climate change that scientists, politicians, and citizens alike should heed. The first international synthesis of butterfly biology in two decades, Butterflies: Ecology and Evolution Taking Flight offers students, scientists, and amateur naturalists a concise overview of the latest developments in the field. Furthermore, it articulates an exciting new perspective of the whole group of approximately 15,000 species of butterflies as a comprehensive model system for all the sciences concerned with biodiversity and its preservation. Contributors: Carol L. Boggs, Paul M. Brakefield, Adriana D. Briscoe, Dana L. Campbell, Elizabeth E. Crone, Mark Deering, Henri Descimon, Erika I. Deinert, Paul R. Ehrlich, John P. Fay, Richard ffrench-Constant, Sherri Fownes, Lawrence E. Gilbert, André Gilles, Ilkka Hanski, Jane K. Hill, Brian Huntley, Niklas Janz, Greg Kareofelas, Nusha Keyghobadi, P. Bernhard Koch, Claire Kremen, David C. Lees, Jean-François Martin, Antónia Monteiro, Paulo César Motta, Camille Parmesan, William D. Patterson, Naomi E. Pierce, Robert A. Raguso, Charles Lee Remington, Jens Roland, Ronald L. Rutowski, Cheryl B. Schultz, J. Mark Scriber, Arthur M. Shapiro, Michael C. Singer, Felix Sperling, Curtis Strobeck, Aram Stump, Chris D. Thomas, Richard VanBuskirk, Hans Van Dyck, Richard I. Vane-Wright, Ward B. Watt, Christer Wiklund, and Mark A. Willis
The internal transcribed spacer 2 (ITS2) of the nuclear ribosomal repeat unit is one of the most commonly applied phylogenetic markers. It is a fast evolving locus, which makes it appropriate for studies at low taxonomic levels, whereas its secondary structure is well conserved, and tree reconstructions are possible at higher taxonomic levels. However, annotation of start and end positions of the ITS2 differs markedly between studies. This is a severe shortcoming, as prediction of a correct secondary structure by standard ab initio folding programs requires accurate identification of the marker in question. Furthermore, the correct structure is essential for multiple sequence alignments based on individual structural features. The present study describes a new tool for the delimitation and identification of the ITS2. It is based on hidden Markov models (HMMs) and verifies annotations by comparison to a conserved structural motif in the 5.8S/28S rRNA regions. Our method was able to identify and delimit the ITS2 in more than 30000 entries lacking start and end annotations in GenBank. Furthermore, 45000 ITS2 sequences with a questionable annotation were re-annotated. Approximately 30000 entries from the ITS2-DB, that uses a homology-based method for structure prediction, were re-annotated. We show that the method is able to correctly annotate an ITS2 as small as 58 nt from Giardia lamblia and an ITS2 as large as 1160 nt from humans. Thus, our method should be a valuable guide during the first and crucial step in any ITS2-based phylogenetic analysis: the delineation of the correct sequence. Sequences can be submitted to the following website for HMM-based ITS2 delineation: http://its2.bioapps.biozentrum.uni-wuerzburg.de.
The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.
The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/.
The relationship of Aricia agestis (Lycaenidae) and its closest relatives in Europe
- Høegh-Guldberg
Høegh-Guldberg, O., 1979. The relationship of Aricia agestis (Lycaenidae) and its
closest relatives in Europe. Nota Lepid. 2, 35-39.
Polyommatus (Aricia) torulensis -eine bisher nicht bekannte lycaenide aus anatolien (Lepidoptera: Lycaenidae)
- Hesselbarth
Hesselbarth, G., Siepe, W., 1993. Polyommatus (Aricia) torulensis -eine bisher nicht
bekannte lycaenide aus anatolien (Lepidoptera: Lycaenidae). Phegea 21 (2), 47-53.
Butterflies of Britain and Europe
- T Tolman
- R Lewington
Tolman, T., Lewington, R., 1997. Butterflies of Britain and Europe. Harper Collins
Publishers, London.