Molecular biological study on speciation and phylogeny of the order Entomobryomorpha (Collembola: Hexapoda)

In order to elucidate the phylogenetic relationship among groups of the order Entomobryomorpha (Collembola), the sequences on the ITS 1 to ITS 2 fragments of the rRNA gene were analyzed in 11 species of three families. In order to avoid the potential risks and inconsistencies of a single method or data set, the phylogenetic reconstructions were based on three different approaches: methods of maximum parsimony, maximum likelihood and neighbor joining. The inferred phylogenies supported monophyly of the order Entomobryomorpha. The relationships between families were different, but the orders of branching within each family were the same. Entomobryidae and Isotomidae were paraphyletic, whereas Tomoceridae was monophyletic. Tomoceridae was subdivided into two branches; the molecular analysis provided results distinctive enough to separate the two genera by the high bootstrap value. On the other hand, two different populations of putative Homidia koreana appeared to be different species, although their chaetotaxy is identical. A wide coverage of characters, including not only morphological characters but also genetic data such as allozymes and DNA sequences, will give a more accurate picture of the classification and phylogeny of the studied group.     

Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola

The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data. Received: 12 January 1996 / Accepted: 10 August 1996     

Phylogeny of Neotropical Seirinae (Collembola,Entomobryidae) based on mitochondrial genomes

Seirinae is one of the most diverse subfamilies of Collembola. To date no detailed phylogeny of Seirinae has been proposed, which leads to difficulties in the understanding of evolutionary patterns regarding this taxon. The main aim of this study is to clarify the phylogenetic relationships within the Neotropical Seirinae, by generating and analysing the mitochondrial genomes of 26 terminal taxa of Entomobryidae, and one species of Paronellidae. Specifically, we first generated Illumina HiSeq 2000 shotgun sequence data from each species, then reconstructed the mitochondrial genome of each species using two methods: MitoZ and MIRA/MITOBim. Using these data, we were able to generate a well-supported phylogeny that combined all the above species as well as three publicly available mitogenomes from other species. Bayesian and maximum likelihood methods were applied using all 13 protein coding genes. In this way, monophyly for the internal groups of Seirinae was obtained based on molecular evidence for the first time, as was the potential validity of three main internal taxa of the subfamily. We furthermore validated that Tyrannoseira is a distinct lineage and propose the elevation of Lepidocyrtinus to genus. Lastly, we anticipate that these newly available mitogenomes will serve as a useful dataset for future studies on the evolution of the Collembola and Hexapoda.     

Brain organization in Collembola (springtails)

Arthropoda is comprised of four major taxa: Hexapoda, Crustacea, Myriapoda and Chelicerata. Although this classification is widely accepted, there is still some debate about the internal relationships of these groups. In particular, the phylogenetic position of Collembola remains enigmatic. Some molecular studies place Collembola into a close relationship to Protura and Diplura within the monophyletic Hexapoda, but this placement is not universally accepted, as Collembola is also regarded as either the sister group to Branchiopoda (a crustacean taxon) or to Pancrustacea (crustaceans + hexapods). To contribute to the current debate on the phylogenetic position of Collembola, we examined the brains in three collembolan species: Folsomia candida, Protaphorura armata and Tetrodontophora bielanensis, using antennal backfills, series of semi-thin sections, and immunostaining technique with several antisera, in conjunction with confocal laser scanning microscopy and three-dimensional reconstructions. We identified several neuroanatomical structures in the collembolan brain, including a fan-shaped central body showing a columnar organization, a protocerebral bridge, one pair of antennal lobes with 20-30 spheroidal glomeruli each, and a structure, which we interpret as a simply organized mushroom body. The results of our neuroanatomical study are consistent with the phylogenetic position of Collembola within the Hexapoda and do not contradict the hypothesis of a close relationship of Collembola, Protura and Diplura.     

Molecular phylogeny of Entomobrya (Collembola: Entomobryidae) from China: Color pattern groups and multiple origins

Highly diversified colorations among springtails (Collembola) have been widely used for species diagnosis, but their phylogenetic significance is poorly known. We addressed this issue in the largest Entomobryinae genus Entomobrya, which possesses variable color patterns among species. The relationships within the genus and to other genera have also rarely been studied. Based on material mainly from China, we have conducted a multilocus phylogeny and topology tests with likelihood and Bayesian algorithms, and accordingly demonstrated the non-monophyly of Chinese Entomobrya. The division of five clades, including Entomobrya and several related genera, coincided well with five types of colorations, respectively. Further analyses of divergence time and historical biogeography revealed that Chinese Entomobrya originated mainly from Palearctic (northern and western) China in the Paleocene and Eocene. This study highlights the great phylo? genetic values as well as taxonomic uses of coloration in Chinese Entomobrya. Multiple phylogenetic and biogeographic origins of Entomobrya imply its complicated relationships with both scaled and unsealed genera of Entomobryinae.     

Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada,Heterotardigrada)

Although morphological characters distinguishing echiniscid genera and species are well understood, the phylogenetic relationships of these taxa are not well established. We thus investigated the phylogeny of Echiniscidae, assessed the monophyly of Echiniscus, and explored the value of cuticular ornamentation as a phylogenetic character within Echiniscus. To do this, DNA was extracted from single individuals for multiple Echiniscus species, and 18S and 28S rRNA gene fragments were sequenced. Each specimen was photographed, and published in an open database prior to DNA extraction, to make morphological evidence available for future inquiries. An updated phylogeny of the class Heterotardigrada is provided, and conflict between the obtained molecular trees and the distribution of dorsal plates among echiniscid genera is highlighted. The monophyly of Echiniscus was corroborated by the data, with the recent genus Diploechiniscus inferred as its sister group, and Testechiniscus as the sister group of this assemblage. Three groups that closely correspond to specific types of cuticular design in Echiniscus have been found with a parsimony network constructed with 18S rRNA data. © 2013 The Linnean Society of London     

Molecular phylogeny of Collembola inferred from ribosomal RNA genes

The classification of taxa within Collembola (Springtails, Hexapoda) has been controversial. In this study, we combined complete 18S rRNA gene with partial 28S rRNA gene (D7-D10) sequences to investigate the phylogeny of Collembola. About 2500 aligned sites of thirty species representing 29 genera from14 families of Collembola were analyzed, including one species of Neelipleona from which no sequence has been reported previously.The phylogenetic trees were obtained by different methods (maximum parsimony, maximum likelihood, and Bayesian analysis). Our results supported the monophyly of two of the four taxonomic groups of Collembola summarized by Deharveng [Deharveng, L., 2004. Recent advances in Collembola systematics. Pedobiologia 48, 415–433.], namely of Poduromorpha and of Symphypleona. Within Poduromorpha, Neanuridae was monophyletic with high support, but Hypogastruridae was not. Entomobryomorpha was paraphyletic, as the Tomoceroidea (Tomoceridae and Oncopoduridae) was found to be apart from the other entomobryomorphs. In the latter Isotomoidea and Entomobryoidea joined into a group with moderate support. Within Symphypleona, the phylogenetic relationship [(Sminthuridae + Bourletiellidae) + Sminthurididae] was consistent with traditional morphological studies. Neelipleona grouped with Symphypleona in all trees, with moderate support in the ML and Bayesian analyses.     

African Dacus (Diptera: Tephritidae: Molecular data and host plant associations do not corroborate morphology based classifications

The genus Dacus Fabricius includes economically important pest fruit flies distributed in the Afrotropical and Indo-Australian regions. Two recent revisions based on morphological characters proposed new and partially discordant classifications synonymizing/revalidating several subgeneric names and forming species groups. Regardless these efforts, the phylogenetic relationships among Dacus species remained largely unresolved mainly because of the difficulties in assigning homologous character states. Therefore we investigated the phylogeny of African Dacus by sequencing 71 representatives of 32 species at two mitochondrial (COI, 16S) and one nuclear (period) gene fragments. Phylogenetic relationships were inferred through Bayesian and Maximum Parsimony methods and hypotheses about the monophyly of Dacus subgenera were tested by Shimodaira–Hasegawa tests. The congruence tests and the analyses of the single gene fragments revealed that the nuclear gene supports similar conclusions as the two mitochondrial genes. Levels of intra- and inter-specific differentiation of Dacus species were highly variable and, in some cases, largely overlapping. The analyses of the concatenated dataset resolved two major bootstrap-supported groups as well as a number of well-supported clades and subclades that often comprised representatives of different subgenera. Additionally, specimens of Dacus humeralis from Eastern and Western African localities formed separate clades, suggesting cryptic differentiation within this taxon. The comparisons between the molecular phylogeny and the morphological classification revealed a number of discrepancies and, in the vast majority of cases, the molecular data were not compatible with the monophyly of the currently recognised subgenera. Conversely, the molecular data showed that Apocynaceae feeders are a monophyletic sister group of species feeding on both Cucurbitaceae and Passifloraceae (these latter being also monophyletic). These results show a clear association between the molecular phylogeny of African Dacus and the evolution of host plant choice and provide a basis towards a more congruent taxonomy of this genus.     

Phylogenetic relationships of the Suidae (Mammalia,Cetartiodactyla): new insights on the relationships within Suoidea

Orliac, M. J., Antoine, P. ‐O., Ducrocq, S. (2010). Phylogenetic relationships of the Suidae (Mammalia, Cetartiodactyla): new insights on the relationships within Suoidea. —Zoologica Scripta, 39, 315–330. In most analyses, both molecular and morphological phylogenies of the Cetartiodactyla support the monophyly of Suoidea. However, the evolutionary history of this superfamily remains poorly known primarily due to long‐lasting debates about the taxonomic content and relationships of the suoid families and subfamilies. Despite their crucial position in the reconstruction of the phylogeny of Cetartiodactyla, Suoidea themselves have received little attention in those phylogenies, and no extensive analysis of the group has been performed so far. We therefore examine the phylogeny of the Suidae through the first phylogenetic analysis of Suoidea, including recent and fossil representatives of all four putative families. The results support the monophyly of the traditional suid subfamilies and indicate the Sanitheriidae as sister taxon to the Suidae clade. The evolutionary history within Suidae reveals its complexity, with major convergences involving important morphological structures such as the auditory region or the upper male canine. Divergent signals gathered from either dental or cranio‐mandibular features are responsible for two long‐lasting unresolved issues within Suoidea: the question of the relationships between ‘Old World’ and ‘New World’ peccaries remaining unsolved, as well as the position and familial status of the mid‐Tertiary tayassuid Perchoerus.     

A molecular phylogeny for digger wasps in the tribe Ammophilini (Hymenoptera,Apoidea, Sphecidae)

The evolution of parental care strategies in aculeate (stinging) wasps and bees has been much studied from a functional perspective, but relatively little phylogenetic information is available to place this in a rigorous historical context, especially at the species level. We used mitochondrial cytochrome oxidase I and two nuclear genes, the elongation factor‐1α and LW rhodopsin, to investigate the phylogeny of Sphecidae digger wasps. We focus particularly on the tribe Ammophilini, a clade of nonsocial apoid wasps that exhibit unusually diverse parental care strategies. We analysed a 2232 bp dataset for 40 ammophilines plus nine other taxa from within the remaining Sphecidae. Our Bayesian phylogeny provides strong support for the monophyly of Ammophilini and for the monophyly of all six individual ammophiline genera, except that the position of P. affinis within the genus Podalonia is only weakly supported. The monophyly of some, but not all, previously designated species groups within the genus Ammophila is supported. We discuss the implications of our results for the evolution of morphological traits used previously in ammophiline systematics.     

Further progress on the phylogeny of Noctuoidea (Insecta: Lepidoptera) using an expanded gene sample

Major progress has been made recently toward resolving the phylogeny of Noctuoidea, the largest superfamily of Lepidoptera. However, numerous questions and weakly supported nodes remain. In this paper we independently check and extend the main findings of multiple recent authors by performing maximum‐likelihood analyses of 5–19 genes (6.7–18.6 kb) in 74 noctuoids representing all the families and a majority of the subfamilies. Our results strongly support the six family system of Zahiri et al., with the former Lymantriidae and Arctiidae subsumed within the huge family Erebidae, and Noctuidae restricted largely to the subfamilies with so‐called trifine hindwing venation. Our data also strongly corroborate monophyly of the set of four families with quadrifid forewing venation, to the exclusion of Notodontidae, and removal from the latter of Oenosandridae. Other among‐family relationships, however, remain unsettled. Our evidence is equivocal on the position of Oenosandridae, which are sister group to either Notodontidae alone or to all other noctuoids. Like other recent nuclear gene studies, our results also provide no strong support for relationships among the four quadrifid forewing families. In contrast, within families our analyses significantly expand the list of robustly resolved relationships, while introducing no strong conflicts with previous molecular studies. Within Notodontidae, for which we present the largest molecular taxon sample to date, we find strong evidence for polyphyly for some, or all, recent definitions of the subfamilies Thaumetopoeinae, Pygaerinae, Notodontinae and Heterocampinae. Deeper divergences are incompletely resolved but there is strong support for multiple ‘backbone’ nodes subtending most of the subfamilies studied. Within Erebidae, we find much agreement and no strong conflict with a recent previous study regarding relationships among subfamilies, and somewhat stronger support. Although many questions remain, the two studies together firmly resolve positions for over half the subfamilies. Within Noctuidae, we find no strong conflict with previous molecular studies regarding relationships among subfamilies, but much stronger resolution along the ‘backbone’ of the phylogeny. Combining information from multiple studies yields strongly resolved positions for most of the subfamilies. Finally, our results strongly suggest that the tribes Pseudeustrotiini and Prodeniini, currently assigned to the largest subfamily, Noctuinae, do not belong there. In sum, our results provide additional corroboration for the main outlines of family‐level phylogeny in Noctuoidea, and contribute toward resolving relationships within families.     

Molecular phylogeny of the family Tephritidae (Insecta: Diptera): New insight from combined analysis of the mitochondrial 12S, 16S,and COII genes

The phylogeny of the family Tephritidae (Diptera: Tephritidae) was reconstructed from mitochondrial 12S, 16S, and COII gene fragments using 87 species, including 79 tephritid and 8 outgroup species. Minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) A sister group relationship between Ortalotrypeta and Tachinisca, and their basal phylogenetic position within Tephritidae; (2) a sister group relationship between the tribe Acanthonevrini and Phytalmiini; (3) monophyly of Plioreocepta, Taomyia and an undescribed new genus, and their sister group relationship with the subfamily Tephritinae; (4) a possible sister group relationship of Cephalophysa and Adramini; and (5) reconfirmation of monophyly for Trypetini, Carpomyini, Tephritinae, and Dacinae. The combination of 12S, 16S, and COII data enabled resolution of phylogenetic relationships among the higher taxa of Tephritidae.     

Distribution pattern and radiation of the European subterranean genus Verhoeffiella (Collembola,Entomobryidae)

One of the most striking features of obligate subterranean species is their narrow distribution ranges. These prevail not only at specific, but often also at generic level. However, some subterranean genera have continental scale and disjunct distribution, which challenges their monophyly and questions the scenarios of their origin and colonization. In our study, we investigated the subterranean collembolan genus Verhoeffiella, currently known from five remote karst regions of Europe. Four nuclear and one mitochondrial genes were assembled to reveal the evolutionary history of the genus. We tested the monophyly of the genus, explored its relationship with putative surface relatives, and its temporal patterns of molecular diversification. The phylogeny revealed a complex relationship of Verhoeffiella with surface species Heteromurus nitidus and partially disentangled the biogeographical question of its disjunct distribution. Further on, several lineages of Verhoeffiella were recognized in the Dinarides, showing highly underestimated diversity and, compared with the number of described species, a sevenfold increase in the number of MOTUs. The radiation is relatively recent, with the events triggering the diversification linked to the Messinian salinity crisis and Pleistocene climatic shifts. The combination of this extensive subterranean radiation and close evolutionary links with epigean relatives makes Verhoeffiella an exceptional case within the subterranean fauna of temperate areas, which significantly contributes to our understanding of subterranean colonization and diversification patterns.     

Molecular phylogeny ofIva (Asteraceae,Heliantheae) based on chloroplast DNA restriction site variation

Iva s.str. (comprising ten species) was examined by cpDNA restriction site variation to determine phyletic relationships within the group. The results were compared with relationships proposed from other data. A total of 86 restriction site mutations was detected, 47 of which proved phylogenetically informative. A single most parsimonious tree was obtained using both Wagner and Dollo parsimony. The tree revealed three main lineages that are congruent with the three chromosome lineages (base numbers of x = 16, 17, 18). The monophyly of the x = 16 and 18 groups was supported strongly by molecular data, while the monophyly of x = 17 lineage was only supported moderately. Relationships among the three lineages indicate that the sect.Iva is paraphyletic because sect.Linearbractea is nested within it. Both morphological data and the secondary chemical data are in agreement with the proposed cpDNA phylogeny. Because of this agreement, sect.Iva is revised such that,I. axillaris was excluded and positioned within the newly proposed sect.Rhizoma. Patterns and rates of cpDNA evolution were also examined. The results indicated an uneven evolution in the chloroplast genome with different rates of cpDNA evolution in at least a few species ofIva. However, the evolutionary clock hypothesis can not be rejected within most of the lineages inIva.     

Higher‐level phylogeny of the insect order Hemiptera: is Auchenorrhyncha really paraphyletic?

The higher‐level phylogeny of the order Hemiptera remains a contentious topic in insect systematics. The controversy is chiefly centred on the unresolved question of whether or not the hemipteran suborder Auchenorrhyncha (including the extant superfamilies Fulgoroidea, Membracoidea, Cicadoidea and Cercopoidea) is a monophyletic lineage. Presented here are the results of a multilocus molecular phylogenetic investigation of relationships among the major hemipteran lineages, designed specifically to address the question of Auchenorrhyncha monophyly in the context of broad taxonomic sampling across Hemiptera. Phylogenetic analyses (maximum parsimony, maximum likelihood and Bayesian inference) were based on DNA nucleotide sequence data from seven gene regions (18S rDNA, 28S rDNA, histone H3, histone 2A, wingless, cytochrome c oxidase I and NADH dehydrogenase subunit 4) generated from 86 in‐group exemplars representing all major lineages of Hemiptera (plus seven out‐group taxa). All combined analyses of these data recover the monophyly of Auchenorrhyncha, and also support the monophyly of each of the following lineages: Hemiptera, Sternorrhyncha, Heteropterodea, Heteroptera, Fulgoroidea, Cicadomorpha, Membracoidea, Cercopoidea and Cicadoidea. Also presented is a review of the major lines of morphological and molecular evidence for and against the monophyly of Auchenorrhyncha.     

Phylogenetic relationships of Hamadryas (Nymphalidae: Biblidinae) based on the combined analysis of morphological and molecular data

A new phylogenetic hypothesis for the Neotropical butterfly genus Hamadryas, based on the combination of a morphological matrix, one mitochondrial (COI) and four nuclear markers (CAD, RpS5, EF1a, and Wingless), is presented. Results from analyses of the molecular evidence are compared with a previously published morphological phylogeny. Molecular data and the analysis of the complete dataset support the monophyly of Hamadryas and most sister groups suggested by morphological data alone. The addition of DNA sequences to the morphological matrix helped define species groups for which no morphological synapomorphies were found. Partitioned Bremer support indicates that COI, CAD, and morphology were consistently in agreement with the combined evidence tree. In contrast, signal from the nuclear markers Rps5, EF1a, and Wingless showed indifference at most levels of the tree, and minor conflict at nodes solving the relationships between species groups. Though resolved, the combined evidence tree shows low resample values, particularly among species groups whose relationships were characterized by short internodes. A reassessment about the pattern of character change for sound production is presented and discussed.     

A phylogenetic analysis of Primulaceae s.l. based on internal transcribed spacer (ITS) DNA sequence data

 Phylogenetic relationships in Primulaceae were investigated by analysis of nuclear rDNA ITS sequences. Thirty-four species of Primulaceae, two of Myrsinaceae and four outgroup taxa were analyzed. In accordance to the results of recently published papers on the phylogeny of Primulaceae we found the family to be paraphyletic and resolved the positions of some genera. Our results show (a) the rather basal position of Centunculus within Lysimachieae, the genus thus being rather distantly related to Anagallis, (b) the close relationship between Lysimachia sect. Lerouxia, Anagallis, Asterolinon, and Pelletiera, (c) the well-supported monophyly of a group consisting of the four genera Hottonia, Omphalogramma, Bryocarpum, and Soldanella, and (d) the affinity of Stimpsonia to the Myrsinaceae-Lysimachieae-Ardisiandra clade. The ITS sequence data do not provide sufficient information to resolve basal relationships within the Primulaceae s.l. There is evidence against the monophyly of the large genera Primula, Androsace, and Lysimachia. In contrast to the phylogenetic reconstructions based on plastid gene sequences, Cyclamen does not appear as a member of the Myrsinaceae-Lysimachieae clade, but its position remains unclear. Revised July 10, 2002; accepted November 21, 2002 Published online: March 20, 2003     

A molecular phylogenetic framework for the subfamily Ocenebrinae (Gastropoda,Muricidae)

The Ocenebrinae is a subfamily of marine predatory gastropods known as oyster and mussel drills. Their current phylogenetic framework is traditionally based on shell and radular characters, but a consensus on relationships among genera is still lacking. We investigated the molecular phylogeny of Ocenebrinae using 50 species and DNA data from one nuclear (28S) and two mitochondrial (COI and 16S) genes, the largest data set so far assembled for this subfamily. We found support for the monophyly of the Ocenebrinae, and species were divided into four major lineages. Within groups, genera had similar geographic distributions, suggesting that except in a few cases, species diversification within clades occurred without range expansions. We discuss the phylogenetic distribution of a labral tooth and a sealed siphonal canal, two characteristic ocenebrine features. We also show that Ocinebrina species in the north‐eastern Pacific are not monophyletic with north‐eastern Atlantic and Mediterranean species, and that the Ocinebrina edwardsii species complex belongs to Ocenebra.