Large amounts of genetic divergence among Italian species of the genus Orchesella (Insecta, collembola) and the relationships of two new species

A revision of the genus Isotomurus (Collembola: Isotomidae) in northern Iran using molecular evidence

Three new species of Isotomurus Börner are described from northern Iran. Status of studied populations is confirmed as new species by using COI and 28SrRNA markers. The new species belong to species-group characterized by 3,3,1 trichobothria on Abd. II–IV, 3+3 laterodistal setae on ventral tube, and no seta on mucro. Isotomurus hyrcanicus sp. nov. is similar to I. palustris Müller in color pattern, but has two lateral bands on last abdominal segments and 10–13 setae on retinaculum. Results of COI analyses shows that all color forms in population of the new species are conspecific. Isotomurus potapovi sp. nov. has a dorsomedial band from Th. II to Abd. V and 6–7 setae on retinaculm, and Isotomurus katule sp. nov. has a uniform body color and 5–8 setae on retinaculum. An identification key for recorded species of genus Isotomurus in Iran is provided. Color pattern as a common character used to identify Isotomurus species is not always reliable and its efficiency needs to be verified for each species.  

Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae)

We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).

Inferring Evolutionary Timescales without Independent Timing Information: An Assessment of "Universal" Insect Rates to Calibrate a Collembola (Hexapoda) Molecular Clock

Previous estimates of nucleotide substitution rates are routinely applied as secondary or “universal” molecular clock calibrations for estimating evolutionary timescales in groups that lack independent timing information. A major limitation of this approach is that rates can vary considerably among taxonomic groups, but the assumption of rate constancy is rarely evaluated prior to using secondary rate calibrations. Here I evaluate whether an insect mitochondrial DNA clock is appropriate for estimating timescales in Collembola—a group of insect-like arthropods characterized by high levels of cryptic diversity. Relative rates of substitution in cytochrome oxidase subunit 1 (COI) were inferred via Bayesian analysis across a topologically constrained Hexapod phylogeny using a relaxed molecular clock model. Rates for Collembola did not differ significantly from the average rate or from the rates estimated for most other groups (25 of 30), suggesting that (1) their apparent cryptic diversity cannot be explained by accelerated rates of molecular evolution and (2) clocks calibrated using “universal” insect rates may be appropriate for estimating evolutionary timescales in this group. However, of the 31 groups investigated, 10 had rates that deviated significantly from the average (6 higher, 4 lower), underscoring the need for caution and careful consideration when applying secondary insect rate calibrations. Lastly, this study exemplifies a relatively simple approach for evaluating rate constancy within a taxonomic group to determine whether the use of secondary rates are appropriate for molecular clock calibrations.

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 phylogenetic 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 unscaled genera of Entomobryinae.

Soil microplastics inhibit the movement of springtail species

Previous studies have indicated the means by which micro-sized plastic particles may affect the soil environment, and this could be linked to the behavior of plastics in the soil system and how these particles are influenced by biological responses. Soil-dwelling organisms play a key role in modifying the soil system by constructing bio-pores, and these structural changes are potentially related to the behavior of plastic particles. In this study, we found that micro-sized plastic particles moved into bio-pores within seconds, and that this influx disrupted the movement of springtails (Lobella sokamensis). The springtails moved to avoid becoming trapped, and this behavior created bio-pores in the soil system. The influx of plastic particles into these cavities subsequently immobilized the springtails within. This phenomenon was observed at low a concentration of plastic particles (8 mg/kg), and it likely occurs in actual soil environments. The findings of this study indicate that the behavior of plastic particles in the soil not only disrupts the movement of springtails but also has wider implications for effective management of soils.

Unusually low genetic divergence at COI barcode locus between two species of intertidal Thalassaphorura (Collembola: Onychiuridae)

Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species. Thalassaphorura thalassophila and Thalassaphorura debilis are among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species. However, their morphological distinctiveness was supported by a molecular divergence much smaller than previously reported at the interspecific level among Collembola. This divergence was even smaller than inter-population divergences recognized in the related edaphic species T. zschokkei, as well as those known between MOTUs within many Collembolan species. Our results may indicate a link between low genetic interspecific divergence and intertidal habitat, as the only biological peculiarity of the two species of interest compared to other Collembolan species analyzed to date is their strict intertidal life.

Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae)

Integrative taxonomic approaches are increasingly providing species-level resolution to ‘cryptic’ diversity. In the absence of an integrative taxonomic approach, formal species validation is often lacking because of inadequate morphological diagnoses. Colouration and chaetotaxy are the most commonly used characters in collembolan taxonomy but can cause confusion in species diagnoses because these characters often have large intraspecific variation. Here, we take an integrative approach to the genus Dicranocentrus in China where four species have been previously recognised, but several members of the genus have been morphologically grouped as a species complex based on having paired outer teeth on unguis and seven colour patterns. Molecular delimitations based on distance- and evolutionary models recovered four candidate lineages from three gene markers and revealed that speciation events likely occurred during the late Neogene (4–13million years ago). Comparison of intact dorsal chaetotaxy, whose homologies were erected on the basis of first instar larva, further validated these candidates as formal species: D. gaoligongensis, sp. nov., D. similis, sp. nov., D. pallidus, sp. nov. and D. varicolor, sp. nov., and increase the number of Dicranocentrus species from China to eight. Our study further highlights the importance of adequate taxonomy in linking morphological and molecular characters within integrative taxonomy.

Distinctive Collembola communities in the Mesovoid Shallow Substratum: First data for the Sierra de Guadarrama National Park (Central Spain) and a description of two new species of Orchesella (Entomobryidae)

Two new species of the genus Orchesella Templeton, 1836 have been identified following intensive sampling in the Colluvial Milieu Souterrain Superficiel (Mesovoid Shallow Substratum, or MSS) of the Sierra de Guadarrama using Subterranean Sampling Devices (SSD). The data were obtained from the first extraction of the traps between May and October of 2015. During a study of the Collembola taxon, 32 different genera (61 species) were identified. The highest representative genus presence in almost all traps was Orchesella, with two new species. One of the two species described had been misidentified until this study was carried out, indicating that their preferential habitat had not been sampled; the second species had never been identified. The community of the Orchesella species in the Colluvial MSS was investigated, leading to the conclusion that this environment has its own assemblage of characteristic species. The opportunity to study specimens that belong to five species of the genus Orchesella, including three previously recollected, has allowed for obtaining reliable information regarding their macrochaetotaxy. A part of this chaetotaxy is proposed as a useful diagnostic tool for the species of the genus. In conclusion, it can be affirmed that this study has demonstrated that the Colluvial Mesovoid Shallow Substratum (Colluvial MSS) has its own fauna, and it supports the hypothesis that it constitutes a new biotope, at least for Collembola.

Delimiting species of Protaphorura (Collembola: Onychiuridae): integrative evidence based on morphology, DNA sequences and geography

Species delimitation remains a significant challenge when the diagnostic morphological characters are limited. Integrative taxonomy was applied to the genus Protaphorura (Collembola: Onychiuridae), which is one of most difficult soil animals to distinguish taxonomically. Three delimitation approaches (morphology, molecular markers and geography) were applied providing rigorous species validation criteria with an acceptably low error rate. Multiple molecular approaches, including distance- and evolutionary model-based methods, were used to determine species boundaries based on 144 standard barcode sequences. Twenty-two molecular putative species were consistently recovered across molecular and geographical analyses. Geographic criteria were was proved to be an efficient delimitation method for onychiurids. Further morphological examination, based on the combination of the number of pseudocelli, parapseudocelli and ventral mesothoracic chaetae, confirmed 18 taxa of 22 molecular units, with six of them described as new species. These characters were found to be of high taxonomical value. This study highlights the potential benefits of integrative taxonomy, particularly simultaneous use of molecular/geographical tools, as a powerful way of ascertaining the true diversity of the Onychiuridae. Our study also highlights that discovering new morphological characters remains central to achieving a full understanding of collembolan taxonomy.

Founder events and pre-glacial divergences shape the genetic structure of European Collembola species

Background

Climate oscillations in the Cenozoic reduced species richness and genetic diversity of terrestrial and aquatic animals and plants in central and northern Europe. The most abundant arthropods in temperate soils are Collembola that live in almost any soil-related habitat. Extant species show little morphological variation to Eocene fossils, suggesting persistence of species in stable habitats for millions of years. Collembola are able to evade adverse climatic conditions by moving into deeper soil layers and are tolerant to frost and draught. If these adaptations sufficed for surviving glacial periods remains open and needs to be investigated in a phylogeographic context, i.e. investigating spatial structure on molecular level. We investigated the molecular variation of three common species of Collembola at a pan-European scale to identify glacial refuges and post-glacial colonization patterns with three genetic markers.

Results

All genes revealed remarkable genetic structure between but not within populations, suggesting density dependent processes for establishment of populations (founder-takes-all principle), which is common for European animals and plants. In contrast to the post-glacial recolonization patterns of many aboveground organisms, divergence times of most geographic lineages indicate preservation of genetic structure since the Miocene.

Conclusions

Collembola survived severe climatic changes including those during Quatenary glaciation and kept high genetic variance across Europe. Likely the buffering of temperature oscilliations in soil and the ability to evade adverse climatic conditions due to cold-tolerance and horizontal migration enabled Collembola to evade strong selective pressure of abiotic forces.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0719-8) contains supplementary material, which is available to authorized users.

Taxonomic review and phylogenetic analysis of fifteen North American Entomobrya (Collembola, Entomobryidae), including four new species

The chaetotaxy of 15 species of eastern North American Entomobrya is redescribed in order to determine potential characters for the diagnosis of cryptic lineages and evaluate the diagnostic and phylogenetic utility of chaetotaxy. As a result, four new species (Entomobrya citrensis Katz & Soto-Adames, sp. n., Entomobrya jubata Katz & Soto-Adames, sp. n., Entomobrya neotenica Katz & Soto-Adames, sp. n. and Entomobrya unifasciata Katz & Soto-Adames, sp. n.) are described, and new diagnoses are provided for Entomobrya assuta Folsom, Entomobrya atrocincta Schött, Entomobrya decemfasciata (Packard), Entomobrya ligata Folsom, Entomobrya multifasciata (Tullberg), and Entomobrya quadrilineata (Bueker). Furthermore, previously undocumented levels of intraspecific variation in macrosetal pattern are reported, tempering the exclusive use of chaetotaxy for species delimitation. Phylogenetic relationships, estimated using both morphological and molecular data, indicate that Entomobrya is likely paraphyletic. The phylogenies also suggest that unreliable character homology, likely fostered by Entomobrya's profusion of macrosetae, may limit the phylogenetic utility of chaetotaxy in groups characterized by an abundance of dorsal macrosetae.

Phylogeny of the genus Palmanura (Collembola: Neanuridae)

In order to assess the phylogenetic structure of the springtail genus Palmanura, as well as to test the monophyly of the tribe Sensillanurini (Neanuridae: Neanurinae), a data matrix of morphological (chaetotactic and other) characters of members of this group was assembled and analysed in the light of Wagner parsimony. The data matrix included all the known members of the Neotropical genus Palmanura, plus representatives of Sensillanura and Americanura. Although not all the clades obtained were highly supported by bootstrap resampling, some structures were relatively constant under different approaches. Alternative analyses (unordered and ordered character states, rescaled weighting procedure) were applied. While alternative solutions were obtained, a number of structures were shared by the results irrespective of the method used. On this basis, the results suggest that some further reassessment is required to confirm formally the monophyly of the tribe Sensillanurini. The genera Palmanura and Americanura are mutually poly/paraphyletic; we thus suggest that Palmanura should be considered as a synonym of Americanura, although some character reassessment and more varied outgroup species may be necessary before a formal generic redefinition can be proposed. Finally, a comparison of the performance of the characters under Wagner parsimony analysis indicated that differences in the characters' retention indexes are due not to the topological (tagmal) position of the traits involved, but to character coding: the characters describing quantitative features (generally numbers of setae) generally performed worse than other types of characters under parsimony. An updated list of the known members of the Sensillanurini (Collembola: Neanuridae: Neanurinae) is presented. © The Willi Hennig Society 2009.

The mitochondrial genomes of Campodea fragilis and Campodea lubbocki (Hexapoda: Diplura): High genetic divergence in a morphologically uniform taxon

Complete mitochondrial genome sequences are presented from two dipluran hexapods (i.e., a group of "primarily wingless insects") of the genus Campodea and compared to those of other arthropods. Their gene order is the same as in most other hexapods and crustaceans. Structural changes have occurred in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2 as well as in both ribosomal RNAs. These mtDNAs have striking biases in nucleotide and amino acid composition. Although the two Campodea species are morphologically highly similar, their genetic divergence is larger than expected, suggesting a long evolutionary history, perhaps under stable ecological conditions.

Genetic structure in Orchesella cincta (Collembola): strong subdivision of European populations inferred from mtDNA and AFLP markers

Population genetic structure is determined both by current processes and historical events. Current processes include gene flow, which is largely influenced by the migration capacity of a species. Historical events are, for example, glaciation periods, which have had a major impact on the distribution of many species. Species with a low capacity or tendency to move about or disperse often exhibit clear spatial genetic structures, whereas mobile species mostly show less spatial genetic differentiation. In this paper we report on the genetic structure of a small, wingless arthropod species (Orchesella cincta: Collembola) in Europe. For this purpose we used mtDNA COII sequences and AFLP markers. We show that large genetic differences exist between populations of O. cincta, as expected from O. cincta's winglessness and sedentary lifestyle. Despite the fact that most variability was observed within populations (59%), a highly significant amount of AFLP variation (25%) was observed between populations from northwestern Europe, central Europe and Italy. This suggests that gene flow among regions is extremely low, which is additionally supported by the lack of shared mtDNA alleles between regions. Based on the genetic variation and sequence differences observed we conclude that the subdivision occurred long before the last glaciation periods. Although the populations still interbreed in the lab, we assume that in the long term the genetic isolation of these regions may lead to speciation processes.

Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes

We evaluated sequence diversity in the mitochondrial cytochrome-c oxidase I (COI; EC 1.9.3.1) gene as a tool for resolving differences among species of Arctic springtails. The Collembola examined in this analysis were collected from Igloolik, Cornwallis, and Somerset islands and included representatives from all major families found in the Arctic. Members of 13 genera and 19 species were examined, including 4 species of the genus Folsomia and 3 species of the genus Hypogastrura. In all cases, species were successfully discriminated. Sequence divergences within species were generally less than 1%, whereas divergences between species were greater than 8% in all cases. Divergences among individuals of one species of Folsomia were much higher (up to 13%), but this likely represents the presence of an undescribed sibling species. We conclude that DNA barcoding is a powerful tool for identifying species of Collembola and should regularly be useful as a complement to traditional, morphological taxonomy.

Islands within an island: phylogeography and conservation genetics of the endangered Hawaiian tree snail Achatinella mustelina

Mitochondrial DNA (mtDNA) sequences were used to evaluate phylogeographic structure within and among populations of three endangered Hawaiian tree snail species (n = 86). The primary focus of this investigation was on setting conservation priorities for Achatinella mustelina. Limited data sets for two additional endangered Hawaiian tree snails, A. livida and A. sowerbyana, were also developed for comparative purposes. Pairwise genetic distance matrices and phylogenetic trees were generated, and an analysis of molecular variance was performed on 675-base pair cytochrome oxidase I gene sequences from multiple populations of Hawaiian tree snails. Sequence data were analysed under distance-based maximum-likelihood, and maximum-parsimony optimality criteria. Within the focal species, A. mustelina, numbers of variable and parsimony informative sites were 90 and 69, respectively. Pairwise intraspecific mtDNA sequence divergence ranged from 0 to 5.3% in A. mustelina, from 0 to 1.0% in A. livida and from 0 to 1.9% in A. sowerbyana. For A. mustelina, population genetic structure and mountain topography were strongly correlated. Maximum genetic distances were observed across deep, largely deforested valleys, and steep mountain peaks, independent of geographical distance. However, in certain areas where forest cover is presently fragmented, little mtDNA sequence divergence exists despite large geographical scales (8 km). Genetic data were used to define evolutionarily significant units for conservation purposes including decisions regarding placement of predator exclusion fences, captive propagation, re-introduction and translocation.

Bridging the "beech-gap": New Zealand invertebrate phylogeography implicates Pleistocene glaciation and Pliocene isolation

The existence of areas of lower endemism and disjunction of New Zealand biota is typified by Nothofagus beech trees (hence "beech-gap") and have been attributed to a variety of causes ranging from ancient fault-mediated displacement (20-25 million years ago) to Pleistocene glacial extirpation (< 1.8 million years ago). We used cytochrome oxidase I and 12S mtDNA sequence data from a suite of endemic invertebrates to explore phylogeographic depth and patterns in South Island, New Zealand, where the "beech-gap" occurs. Phylogeographic structure and genetic distance data are not consistent with ancient vicariant processes as a source of observed pattern. However, we also find that phylogeographic patterns are not entirely congruent and appear to reflect disparate responses to fragmentation, which we term "gap," "colonization," and "regional." Radiations among congenerics, and in at least one instance within a species, probably took place in the Pliocene (2-7 million years ago), possibly under the influence of the onset of mountain building. This orogenic phase may have had a considerable impact on the development of the biota generally. Some of the taxa that we studied do not appear to have suffered range reduction during Pleistocene glaciation, consistent with their survival throughout that epoch in alpine habitats to which they are adapted. Other taxa have colonized the beech-gap recently (i.e., after glaciation), whereas few among our sample retain evidence of extirpation in the most heavily glaciated zone.