Molecular phylogenetic analysis of the dragonfly genera Libellula, Ladona, and Plathemis (Odonata: Libellulidae) based on mitochondrial cytochrome oxidase I and 16S rRNA sequence data

Genetic diversity and phylogeographic patterns of the peacock jewel-damselfly, Rhinocypha fenestrella (Rambur, 1842)

Despite is known to have widespread distribution and the most active species of the family Chlorocyphidae, the molecular data of Rhinocypha fenestrella (Rambur, 1842) are relatively scarce. The present study is the first that examined the genetic diversity and phylogeographic pattern of the peacock jewel-damselfly R. fenestrella by sequencing the cytochrome C oxidase I (cox1) and 16S rRNA gene regions from 147 individuals representing eight populations in Malaysia. A total of 26 and 10 unique haplotypes were revealed by the cox1 and 16S rRNA genes, respectively, and 32 haplotypes were recovered by the concatenated sequences of cox1+16S. Analyses indicated that haplotype AB2 was the most frequent and the most widespread haplotype in Malaysia while haplotype AB1 was suggested as the common ancestor haplotype of the R. fenestrella that may arose from the Negeri Sembilan as discovered from cox1+16S haplotype network analysis. Overall haplotype and nucleotide diversities of the concatenated sequences were Hd = 0.8937 and Pi = 0.0028, respectively, with great genetic differentiation (FST = 0.6387) and low gene flow (Nm = 0.14). Population from Pahang presented the highest genetic diversity (Hd = 0.8889, Pi = 0.0022, Nh = 9), whereas Kedah population demonstrated the lowest diversity (Hd = 0.2842, Pi = 0.0003, Nh = 4). The concatenated sequences of cox1+16S showed genetic divergence ranging from 0.09% to 0.97%, whereas the genetic divergence for cox1 and 16S rRNA genes were 0.16% to 1.63% and 0.01% to 0.75% respectively. This study provides for the first-time insights on the intraspecific genetic diversity, phylogeographic pattern and ancestral haplotype of Rhinocypha fenestrella. The understanding of molecular data especially phylogeographic pattern can enhance the knowledge about insect origin, their diversity, and capability to disperse in particular environments.

Quaternary Vicariance of Lotic Coeliccia in the Ryukyu-Taiwan Islands Contrasted with Lentic Copera

Lotic dragonflies and damselflies are expected to be more affected by vicariance than lentic sister species. We demonstrated that severe vicariant speciation acted on lotic Coeliccia in contrast to lentic Copera damselflies, which are both included in the family Platycnemididae. We constructed maximum likelihood and Bayesian inference trees of these Platycnemididae species from the continental islands of Ryukyu (Amami, Okinawa, and Yaeyama islands), Taiwan, and Japan relative to Chinese species using raxmlGUI and BEAST, based on the mitochondrial COI gene (682 bp), COII gene (494 bp), 16SrRNA (478 bp), and the nuclear 28SrRNA gene (807 bp). In BEAUti, we calibrated the splitting age of the MRCA of all the Coeliccia species as 1.55-0.15 million years ago (Ma), a date that corresponds to a geologic constraint: the Okinawa trough and associated straits, including the Yilan basin in Taiwan, began to rift at 1.55 Ma, isolating the Ryukyu-Taiwan islands from the Chinese continent. The vicariance split Coeliccia into the Ryukyu-side clade of Coeliccia ryukyuensis (Coe. r. ryukyuensis in Okinawa and Coe. r. amamii in Amami) and Coeliccia flavicauda (Coe. f. masakii in Yaeyama and Coe. f. flavicauda in southern Taiwan), and the Chinese-side clade of Coeliccia cyanomelas (northern Taiwan and China), separated by the Okinawa trough. These Coeliccia species were further deeply differentiated to form local populations on the major islands and some of the minor islands. The Copera clade constituted a sister of the lotic Coeliccia clade, but genetic differentiation was not recognizable in lentic Copera between China, Taiwan, and Japan. Base substitution rates applying a strict clock model were estimated for COI: 0.0783, COII: 0.0803, 18SrRNA: 0.0186, 28SrRNA: 0.00577, and combined: 0.0408 substitutions/site/myr, and these rates are relatively high.

Genetic interaction and diversity of the families Libellulidae and Gomphidae through COI gene from China and Pakistan

A total of 300 dragonflies (Odonata) were collected from six different localities of China and Pakistan. Sixty seven representative samples were selected to sequence their mitochondrial cytochrome oxidase subunit I (COI). An examination of the resultant sequences identified 21 different dragonfly species, belonging to 15 distinct genera, two families, Libellulidae and Gomphidae. Sequence alignment was executed using Clustal-W in BioEdit v6. The phylogenetic tree was constructed through Neighbor-joining method by using Jukes-Cantor model, and genetic divergence was calculated via Kimura 2-parameter using MEGA7, while Genetic diversity was calculated by DnaSP v5. The maximum genetic divergence was observed for Crocothemis servilia, at 20.49%, followed by Libellulidae sp. with 22.30% while minimum divergence (0.82%) was observed for Melligomphus ardens. Likewise, a significant genetic diversity was observed for all species. However, Crocothemis servilia species presented maximum value (176 mutations) followed by Libellulidae spp. (150 mutations), whereas minimum value (3 mutations) was observed by Orthetrum testaceum. Interestingly, the diversity of C. servilia, all of which are collected from a single location of China, is much higher than those from Pakistan, which were collected from 5 different places with a spatial distance exceeding 500 Kms. Our results are useful in gaining a full appreciation of the global diversity of dragonflies and the development of conservation measures of this insect.

Molecular phylogeny of Orthetrum dragonflies reveals cryptic species of Orthetrum pruinosum

Dragonflies of the genus Orthetrum are members of the suborder Anisoptera, family Libellulidae. There are species pairs whose members are not easily separated from each other by morphological characters. In the present study, the DNA nucleotide sequences of mitochondrial and nuclear genes were employed to elucidate the phylogeny and systematics of Orthetrum dragonflies. Phylogenetic analyses could not resolve the various subfamilies of the family Libellulidae unequivocally. The nuclear 28S rRNA gene is highly conserved and could not resolve congeneric species of Orthetrum. Individual mitochondrial genes (COI, COII, and 16S rRNA) and combination of these genes as well as the nuclear ITS1&2 genes clearly differentiate morphologically similar species, such as the reddish species pairs O. chrysis and O. testaceum, and the bluish-coloured species O. glaucum and O. luzonicum. This study also reveals distinct genetic lineages between O. pruinosum schneideri (occurring in Malaysia) and O. pruinosum neglectum (occurring north of Peninsular Malaysia from India to Japan), indicating these taxa are cryptic species.

Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences

Even when the maximum likelihood (ML) tree is a better estimate of the true phylogenetic tree than those produced by other methods, the result of a poor ML search may be no better than that of a more thorough search under some faster criterion. The ability to find the globally optimal ML tree is therefore important. Here, I compare a range of heuristic search strategies (and their associated computer programs) in terms of their success at locating the ML tree for 20 empirical data sets with 14 to 158 sequences and 411 to 120,762 aligned nucleotides. Three distinct topics are discussed: the success of the search strategies in relation to certain features of the data, the generation of starting trees for the search, and the exploration of multiple islands of trees. As a starting tree, there was little difference among the neighbor-joining tree based on absolute differences (including the BioNJ tree), the stepwise-addition parsimony tree (with or without nearest-neighbor-interchange (NNI) branch swapping), and the stepwise-addition ML tree. The latter produced the best ML score on average but was orders of magnitude slower than the alternatives. The BioNJ tree was second best on average. As search strategies, star decomposition and quartet puzzling were the slowest and produced the worst ML scores. The DPRml, IQPNNI, MultiPhyl, PhyML, PhyNav, and TreeFinder programs with default options produced qualitatively similar results, each locating a single tree that tended to be in an NNI suboptimum (rather than the global optimum) when the data set had low phylogenetic information. For such data sets, there were multiple tree islands with very similar ML scores. The likelihood surface only became relatively simple for data sets that contained approximately 500 aligned nucleotides for 50 sequences and 3,000 nucleotides for 100 sequences. The RAxML and GARLI programs allowed multiple islands to be explored easily, but both programs also tended to find NNI suboptima. A newly developed version of the likelihood ratchet using PAUP* successfully found the peaks of multiple islands, but its speed needs to be improved.

Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata

DNA barcoding has become a promising means for identifying organisms of all life stages. Currently, phenetic approaches and tree-building methods have been used to define species boundaries and discover 'cryptic species'. However, a universal threshold of genetic distance values to distinguish taxonomic groups cannot be determined. As an alternative, DNA barcoding approaches can be 'character based', whereby species are identified through the presence or absence of discrete nucleotide substitutions (character states) within a DNA sequence. We demonstrate the potential of character-based DNA barcodes by analysing 833 odonate specimens from 103 localities belonging to 64 species. A total of 54 species and 22 genera could be discriminated reliably through unique combinations of character states within only one mitochondrial gene region (NADH dehydrogenase 1). Character-based DNA barcodes were further successfully established at a population level discriminating seven population-specific entities out of a total of 19 populations belonging to three species. Thus, for the first time, DNA barcodes have been found to identify entities below the species level that may constitute separate conservation units or even species units. Our findings suggest that character-based DNA barcoding can be a rapid and reliable means for (i) the assignment of unknown specimens to a taxonomic group, (ii) the exploration of diagnosability of conservation units, and (iii) complementing taxonomic identification systems.

Phylogeny of the higher Libelluloidea (Anisoptera: Odonata): An exploration of the most speciose superfamily of dragonflies

Although libelluloid dragonflies are diverse, numerous, and commonly observed and studied, their phylogenetic history is uncertain. Over 150 years of taxonomic study of Libelluloidea Rambur, 1842, beginning with Hagen (1840), [Rambur, M.P., 1842. Neuropteres. Histoire naturelle des Insectes, Paris, pp. 534; Hagen, H., 1840. Synonymia Libellularum Europaearum. Dissertation inaugularis quam consensu et auctoritate gratiosi medicorum ordinis in academia albertina ad summos in medicina et chirurgia honores.] and Selys (1850), [de Selys Longchamps, E., 1850. Revue des Odonates ou Libellules d'Europe [avec la collaboration de H.A. Hagen]. Muquardt, Bruxelles; Leipzig, 1-408.], has failed to produce a consensus about family and subfamily relationships. The present study provides a well-substantiated phylogeny of the Libelluloidea generated from gene fragments of two independent genes, the 16S and 28S ribosomal RNA (rRNA), and using models that take into account non-independence of correlated rRNA sites. Ninety-three ingroup taxa and six outgroup taxa were amplified for the 28S fragment; 78 ingroup taxa and five outgroup taxa were amplified for the 16S fragment. Bayesian, likelihood and parsimony analyses of the combined data produce well-resolved phylogenetic hypotheses and several previously suggested monophyletic groups were supported by each analysis. Macromiinae, Corduliidae s. s., and Libellulidae are each monophyletic. The corduliid (s.l.) subfamilies Synthemistinae, Gomphomacromiinae, and Idionychinae form a monophyletic group, separate from the Corduliinae. Libellulidae comprises three previously accepted subfamilies (Urothemistinae, a very restricted Tetrathemistinae, and a modified Libellulinae) and five additional consistently recovered groups. None of the other previously proposed subfamilies are supported. Bayesian analyses run with an additional 71 sequences obtained from GenBank did not alter our conclusions. The evolution of adult and larval morphological characters is discussed here to suggest areas for future focus. This study shows the inherent problems in using poorly defined and sometimes inaccurately scored characters, basing groups on symplesiomorphies, and failure to recognize the widespread effects of character correlation and convergence, especially in aspects of wing venation.

Phylogenetic relationships, divergence time estimation, and global biogeographic patterns of calopterygoid damselflies (odonata, zygoptera) inferred from ribosomal DNA sequences

The calopterygoid superfamily (Calopterygidae + Hetaerinidae) is composed of more than twenty genera in two families: the Calopterygidae (at least 17) and the Hetaerinidae (at least 4). Here, 62 calopterygoid (ingroup) taxa representing 18 genera and 15 outgroup taxa are subjected to phylogenetic analysis using the ribosomal 18S and 5.8S genes and internal transcribed spacers (ITS1, ITS2). The five other families of calopterid affinity (Polythoridae, Dicteriadidae, Amphipterygidae, Euphaeidae, and Chlorocyphidae) are included in the outgroup. For phylogenetic inference, we applied maximum parsimony, maximum likelihood, and the Bayesian inference methods. A molecular phylogeny combined with a geographic analysis produced a well-supported phylogenetic hypothesis that partly confirms the traditional taxonomy and describes distributional patterns. A monophyletic origin of the calopterygoids emerges, revealing the Hetaerinid clade as sister group to the Calopterygidae sensu strictu. Within Calopterygidae, seven clades of subfamily rank are recognized. Phylogenetic dating was performed with semiparametric rate smoothing by penalized likelihood, using seven reference fossils for calibration. Divergence time based on the ribosomal genes and spacers and fossil constraints indicate that Calopteryginae (10 genera, approximately 50% of all Calopterygid taxa studied here), Vestalinae (1 genus), and Hetaerinidae (1 genus out of 4 studied here) started radiating around 65 Mya (K/T boundary). The South American Iridictyon (without distinctive morphology except for wing venation) and Southeast Asian Noguchiphaea (with distinctive morphology) are older (about 86 My) and may be survivors of old clades with a Gondwanian range that went extinct at the K/T boundary. The same reasoning (and an even older age, ca. 150 My) applies to the amphipterygids Rimanella and Pentaphlebia (South America-Africa). The extant Calopterygidae show particular species and genus richness between west China and Japan, with genera originating between the early Oligocene and Pleistocene. Much of that richness probably extended much wider in preglacial times. The Holarctic Calopteryx, of Miocene age, was deeply affected by the climatic cooling of the Pliocene and by the Pleistocene glaciations. Its North American and Japanese representatives are of Miocene and Pliocene age, respectively, but its impoverished Euro-Siberian taxa are late Pliocene-Pleistocene, showing reinvasion, speciation, and introgression events. The five other calopterid families combine with the Calopterygidae and Hetaerinidae to form the monophyletic cohort Caloptera, with Polythoridae, Dicteriadidae, and Amphipterygidae sister group to Calopterygoidea. The crown node age of the latter three families has an age of about 157 My, but the Dicteriadidae and Polythoridae themselves are of Eocene age, and the same is true for the Euphaeidae and Chlorocyphidae. The cohort Caloptera itself, with about 197 My of age, goes back to the early Jurassic.