查看更多>>摘要：Abstract The field of molecular phylogenetics is being revolutionized with next‐generation sequencing technologies making it possible to sequence large numbers of genomes for non‐model organisms ushering us into the era of phylogenomics. The current challenge is no longer how to get enough data, but rather how to analyse the data and how to assess the support for the inferred phylogeny. Here, we focus on one of the largest animal groups on the planet – butterflies and moths (order Lepidoptera), whose phylogeny remains unresolved despite several recent phylogenomic studies. In this study, we assess the potential causes and consequences of the conflicting phylogenetic hypotheses. With a dataset consisting of 331 protein‐coding genes and the alignment length over 290,000 base pairs, including 200 taxa representing 83% of lepidopteran superfamilies, we compare phylogenetic hypotheses inferred from amino acid and nucleotide alignments. The resulting two phylogenies are discordant, especially with respect to the placement of the superfamily Gelechioidea, which is likely due to compositional bias and possible other model violations. Furthermore, we employed a series of analyses to dissect our dataset and demonstrate that there is sufficient phylogenetic signal to resolve much – but not all – of the lepidopteran tree of life. The relationships among superfamilies within Ditrysia, the most species rich lepidopteran clade containing 98% of the extant species, remain poorly resolved. We conclude that taxon sampling remains an issue even in phylogenomic analyses and recommend that poorly sampled highly diverse groups, such as Gelechioidea in Lepidoptera, should receive extra attention in the future.
Vladimir M. GnezdilovFedor V. KonstantinovAnna A. Namyatova
18页
查看更多>>摘要：Abstract The Issidae are highly diverse in terms of morphology and species richness. Despite recent efforts, the internal phylogeny and classification of this planthopper family remain controversial. Here, we present a phylogeny of the family inferred with Bayesian and Maximum Likelihood analyses of a nine‐gene molecular dataset (4702?bp) and morphological data (35 characters) across a broad sample of taxa (99 terminals). Based on these results, we verify the taxonomic status of the issid subfamilies, tribes and generic complexes. Results revealed a well‐supported basal dichotomy of the family into two clades, corresponding to the subfamilies Issinae and Hysteropterinae. Within Issinae, the tribes Issini, Thioniini, Sarimini, Hemisphaeriini, Parahiraciini and Kodaianellini were recovered with high support. Four strongly statistically supported clades were revealed within the subfamily Hysteropterinae, but we refrain from taxonomic decisions in the absence of morphological characters to diagnose the clades A–C. Interestingly, the obtained results are in good agreement with L. Melichar's view on Issidae classification suggested more than a century ago. Our results challenge an early Cretaceous origin of the Issidae and the basal split of the family between Neotropical taxa (Thioniini) and the remaining issids.
查看更多>>摘要：Abstract Meloidae is a beetle family with about 3000 species divided into three subfamilies and 16 tribes. Included is the tribe Lyttini containing 33 genera and about 400 species. However, the boundaries of Lyttini have proved hard to define since the systematics of this tribe have repeatedly changed. In this study, we investigated the phylogeny of Lyttini and tested for its monophyly based on a comprehensive molecular dataset of mitochondrial (COI and 16S) and nuclear (CAD and 28S) genes including 57 genera and 385 species representing most of the tribes of Meloidae. Further phylogenetic analyses were performed on a reduced taxon set (51 genera and 135 species covering 60% of the generic diversity of Lyttini) in order to maximize the number of loci and minimize missing data. Phylogenetic results strongly supported the monophyly of most of the tribes of the subfamily Meloinae, apart from Lyttini, which is split into 11 phylogenetically distinct lineages scattered throughout the tree. Based on these results, we restrict the tribe Lyttini to the genera Alosimus Mulsant, Lydus Dejan, Lytta Fabricius, Muzimes Mulsant & Rey and Oenas Latreille, all exclusive to the Holarctic region. The relationships among the remaining genera previously included in Lyttini and the other 10 lineages representing ‘non‐Lyttini’ tribes remain to be clarified. This study also provides a number of nomenclatural acts [including Pseudolytta n. stat.; Lytta (Taurilytta) n. subgen.; Lytta (Teratolytta) n.stat.; Mimovesperus resurrected; Denierella?=?Epicauta n.syn.; Psalydolytta?=?Epicauta n. syn.] and working hypotheses for future investigations on the systematics of Meloidae.
查看更多>>摘要：Abstract Termites are social cockroaches distributed throughout warm temperate and tropical ecosystems. The ancestor of modern termites roamed the earth during the early Cretaceous, suggesting that both vicariance and overseas dispersal may have shaped the distribution of early diverging termites. We investigate the historical biogeography of three early diverging termite families –Stolotermitidae, Hodotermitidae and Archotermopsidae (clade Teletisoptera) – using the nuclear rRNA genes and mitochondrial genomes of 27 samples. Our analyses confirm the monophyly of Teletisoptera, with Stolotermitidae diverging from Hodotermitidae + Archotermopsidae approximately 100?Ma. Although Hodotermitidae are monophyletic, our results demonstrate the paraphyly of Archotermopsidae. Phylogenetic analyses indicate that the timing of divergence among the main lineages of Hodotermitidae + Archotermopsidae are compatible with vicariance. In the Stolotermitidae, however, the common ancestors of modern Porotermes Hagen and Stolotermes Hagen are roughly as old as 20 and 35?Ma, respectively, indicating that the presence of these genera in South America, Africa and Australia involved over‐water dispersals. Overall, our results suggest that early diverging termite lineages acquired their current distribution through a combination of over‐water dispersals and dispersal via land bridges. We clarify the classification by resolving the paraphyly of Archotermopsidae, restricting the family to Archotermopsis Desneux and Zootermopsis Emerson and elevating Hodotermopsinae (Hodotermopsis Holmgren) as Hodotermopsidae (status novum).
查看更多>>摘要：Abstract The use of mitochondrial markers for taxonomic identification and biodiversity monitoring is not without risks or limitations. Most importantly, the natural transfer of DNA from the mitochondria to the nucleus generates nonfunctional nuclear copies of mitochondrial DNA (NUMTs). Their abundance and size vary significantly among taxa, and NUMTs have been reported to complicate molecular studies based on mitochondrial markers in several insect orders, most prominently in Orthoptera. The significance of this phenomenon in Odonata has not yet been properly addressed. Here, we present a complete mitochondrial genome and a draft nuclear genome of Leucorrhinia albifrons (Odonata: Libellulidae), as well as NUMT and cox1 sequences from the related species Leucorrhinia dubia. We document the presence of NUMTs in the L. albifrons nuclear genome and in nuclear genomes of two other Odonata species available in public databases. Our results show that NUMTs can have a serious impact on barcoding, phylogenetic, population and phylogeographic studies of Odonata, especially when the barcode is located in the cox1 gene, the most frequently used molecular marker for Odonata. We suggest that nad1 should be used alone or in combination with cox1 to minimize unintended confusion with NUMTs. Finally, we present a mitophylogenomic analysis of Odonata and document several cases of misidentified mitochondrial genomes belonging to species different from those indicated in public databases. In conclusion, our findings represent an important step for future metabarcoding studies of Odonata based on mitochondrial DNA markers.
?ubo? HrivniakPavel SrokaRoman J. GodunkoPeter Manko...
15页
查看更多>>摘要：Abstract The evolution and distribution of mountain biota are closely linked with mountain formation and topographic complexity. Here we explore the diversification of cold‐tolerant mayflies of the subgenus Epeorus (Caucasiron) in the south‐eastern Greater Caucasus, an area of dynamic changes in topography since the Miocene, driven by the convergence of the Greater and Lesser Caucasus. We hypothesized that orogenic processes promoted the diversification of E. (Caucasiron) and that the resultant diversification pattern followed the timing and progress of mountain formation along the range. A new evolutionary lineage of E. (Caucasiron) distributed in the central‐eastern Greater Caucasus was found and described as Epeorus (Caucasiron) tripertitus sp.n. It consists of three clades clearly differentiated based on mitochondrial sequence data, but indistinguishable by morphological traits. Based on a time‐calibrated phylogeny using mitochondrial (COI, 16S) and nuclear (EF, wg, 28S) markers, we found that a gradual allopatric diversification of the ancestral population of E. (C.) tripertitus sp.n. dated to a period lasting from the late Miocene to the Pleistocene spread eastward along the range. This pattern corresponded with the process of topographic deformation which started in the central part of the range in the Miocene and progressed to the east during the Pliocene/Pleistocene. The results implied the dominant role of mountain building on the biotic diversification of this region and continuing recent speciation in the south‐eastern part of the mountains.
Rolf G. BeutelDi LiFrank FriedrichKenny Jandausch...
19页
查看更多>>摘要：Abstract Moth lacewings (Ithonidae) are a rare group of Neuroptera with an unusual subterranean larval life‐style. We examined external and internal head structures of an older‐instar larva of Ithone Newman with a broad spectrum of techniques. Larval autapomorphies, likely correlated with the subterranean habits, are the compact and shovel‐shaped head, unusually massive mandibular‐maxillary stylets, and a C‐shaped postcephalic body. Other cephalic autapomorphies are the massive X‐shaped tentorium, incurved antennae, and a strongly developed M. verticopharyngalis. The visual organs are distinctly simplified but a single functional stemma on each side of head is retained despite of the subterranean habits. In contrast to previous studies, a well‐developed gular sclerite is present in Ithonidae, possibly a secondary acquisition. A cephalic gland complex and poison channel are present, with an unexpected additional lateral accessory gland and an additional lateral channel. The poison glands and dual channels very clearly indicate that the larvae are predators, contradicting the phytophagous habits formerly postulated. Compared with soil‐inhabiting scarabaeoid beetle larvae, striking differences of head structures are due to different feeding habits and phylogenetic constraints. Morphological similarities like a C‐shaped postcephalic body and strongly developed legs suitable for burrowing in soil are evolutionary parallels associated with the subterranean life‐style in the two non‐related groups. Bayesian phylogenetic analysis was carried out with an updated morphological matrix. The results were compared with a phylogeny based on anchored hybrid enrichment data. The evolutionary transformations of selected characters were evaluated using phylogenies estimated from both datasets.
查看更多>>摘要：Abstract Parapatrically distributed taxa pose a challenge for species delimitation due to the presence of gene flow and inherent arbitrariness of exactly defining the species boundaries in such systems. We tackled the problem of species delimitation in a parapatric species pair of Melitaea butterflies using two popular genomic methods—double digest restriction‐site associated DNA sequencing (ddRAD) and target enrichment. We compared newly generated target enrichment dataset with 1733 loci to the already available ddRAD data from a previous study on the same set of specimens using a suite of phylogenetic, population genetic, and species delimitation methods. We recovered consistent phylogenetic relationships across the datasets, both demonstrating the presence of a genetically distinct Balkan lineage and paraphyly of Melitaea athalia with respect to Melitaea celadussa. Population genetic STRUCTURE analyses supported the presence of two species when using ddRAD data, but three species when using target enrichment, while a Bayes factor delimitation analysis found both two and three species scenarios equally decisive in both datasets. As the results obtained from both methods were largely congruent, we discuss some practical considerations and benefits of target enrichment over RAD sequencing. We conclude that the choice of method of genomic data collection does not influence the results of phylogenetic analyses at alpha taxonomic level, given a sufficient number of loci. Finally, we recommend a solution for delineating species in parapatric scenarios by proposing that parapatric taxa be consistently classified as subspecies or complete species, but not both, to promote taxonomic stability.
查看更多>>摘要：Abstract Paleotropical clades with largely disjunct distributions are ideal models for biogeographic reconstructions. The dung beetle genera Grebennikovius Mlambo, Scholtz & Deschodt, Epactoides Olsouffief and Ochicanthon Vaz‐de‐Mello are distributed in Tanzania, Madagascar and Réunion, and the Oriental region, respectively. We combine morphology and molecular dataset to reconstruct the phylogenetic relationships between these taxa. Our analyses corroborate previous hypotheses of monophyly of the group, which is here described as new tribe Epactoidini trib. nov. Grebennikovius is recovered as sister to Epactoides, while Ochicanthon emerges as sister to them both. The disjunct distribution of our focal clade is unusual within the subfamily Scarabaeinae. Bayesian divergence time estimates and ancestral range reconstructions indicate an African origin of the crown group of the tribe Epactoidini trib. nov. in the early mid Eocene, ca. 46?Ma. The divergence between Epactoides and its sister is dated to 32.3?Ma, while the crown age for the genus Ochicanthon is dated to 27?Ma. We investigate the factors that may have shaped the current distribution of the tribe Epactoidini trib. nov. The formation of the Gomphotherium landbridge, along with favourable environmental conditions would have allowed dry‐intolerant organisms, such as Ochicanthon, to disperse out of Africa. Remarkable climatic stability of the Eastern Arc Mountains was critical for the retention of the monotypic genus Grebennikovius. We suggest two subsequent overwater dispersal events: the migration of the most recent common ancestor (MRCA) of Epactoides from Africa to Madagascar (32.3–29.5?Ma); the lately dispersal of the MRCA of the today's extinct Epactoides giganteus Rossini, Vaz‐de‐Mello & Montreuil to Réunion island from Madagascar (3.4?Ma). We suggest that the high potential of dispersal of Epactoidini trib. nov. dung beetles and the strict association to forest habitat might have triggered two major radiations, one in Madagascar and one in the Oriental Region.
NSTL
Wiley