Sympatric occurrence of diverged mtDNA lineages of Pityogenes chalcographus (Coleoptera, Scolytinae) in Europe

Two sympatric lineages of Australian Cnestus solidus share Ambrosiella symbionts but not Wolbachia

Sympatric lineages of inbreeding species provide an excellent opportunity to investigate species divergence patterns and processes. Many ambrosia beetle lineages (Curculionidae: Scolytinae) reproduce by predominant inbreeding through sib mating in nests excavated in woody plant parts wherein they cultivate symbiotic ambrosia fungi as their sole source of nutrition. The Xyleborini ambrosia beetle species Cnestus solidus and Cnestus pseudosolidus are sympatrically distributed across eastern Australia and have overlapping morphological variation. Using multilocus sequencing analysis of individuals collected from 19 sites spanning their sympatric distribution, we assessed their phylogenetic relationships, taxonomic status and microbial symbionts. We found no genetic differentiation between individuals morphologically identified as C. solidus and C. pseudosolidus confirming previous suggestions that C. pseudosolidus is synonymous to C. solidus. However, within C. solidus we unexpectedly discovered the sympatric coexistence of two morphologically indistinguishable but genetically distinct lineages with small nuclear yet large mitochondrial divergence. At all sites except one, individuals of both lineages carried the same primary fungal symbiont, a new Ambrosiella species, indicating that fungal symbiont differentiation may not be involved in lineage divergence. One strain of the maternally inherited bacterial endosymbiont Wolbachia was found at high prevalence in individuals of the more common lineage but not in the other, suggesting that it may influence host fitness. Our data suggest that the two Australian Cnestus lineages diverged allopatrically, and one lineage then acquired Wolbachia. Predominant inbreeding and Wolbachia infection may have reinforced reproductive barriers between these two lineages after their secondary contact contributing to their current sympatric distribution.

Evolutionary ecology of the bark beetles Ips typographus and Pityogenes chalcographus

Ips typographus (L.) and Pityogenes chalcographus (L.) (Coleoptera: Curculionidae) are two common bark beetle species on Norway spruce in Eurasia. Multiple biotic and abiotic factors affect the life cycles of these two beetles, shaping their ecology and evolution. In this article, we provide a comprehensive and comparative summary of selected life-history traits. We highlight similarities and differences in biotic factors, like host range, interspecific competition, host colonization, reproductive behaviour and fungal symbioses. Moreover, we focus on the species' responses to abiotic factors and compare their temperature-dependent development and flight behaviour, cold adaptations and diapause strategies. Differences in biotic and abiotic traits might be the result of recent, species-specific evolutionary histories, particularly during the Pleistocene, with differences in glacial survival and postglacial recolonization. Finally, we discuss future research directions to understand ecological and evolutionary pathways of the two bark beetle species, for both basic research and applied forest management.

Sympatric occurrence of deeply diverged mitochondrial DNA lineages in Siberian geometrid moths (Lepidoptera: Geometridae): cryptic speciation, mitochondrial introgression, secondary admixture or effect of Wolbachia?

The divergent sympatric mitochondrial lineages within traditionally recognized species present a challenge regularly faced by taxonomists and evolutionary biologists. We encountered this problem when studying the Siberian geometrid moths, Alcis deversata and Thalera chlorosaria. Within each of these species we found two deeply diverged mitochondrial lineages that demonstrated a level of genetic differentiation exceeding the standard interspecific DNA barcode threshold. Using analyses of nuclear genes, morphology, ecological preferences and Wolbachia endosymbionts, we tested five hypotheses that might explain the mitochondrial pattern observed: cryptic speciation, ancestral polymorphism, interspecific mitochondrial introgression, secondary admixture of allopatrically evolved populations and an effect of intracellular Wolbachia endosymbionts. We demonstrate that in A. deversata and Th. chlorosaria the mitochondrial differences are not correlated with differences in nuclear genes, morphology, ecology and Wolbachia infection status, thus not supporting the hypothesis of cryptic species and an effect of Wolbachia. Mitochondrial introgression can lead to a situation in which one species has both its own mitochondrial lineage and the lineage obtained from another species. We found this situation in the species pair Alcis repandata and Alcis extinctaria. We conclude that the mitochondrial heterogeneity in A. deversata and Th. chlorosaria is most likely to be attributable to the secondary admixture of allopatrically evolved populations.

The Apennines as a cryptic Pleistocene refugium of the bark beetle Pityogenes chalcographus (Coleoptera: Curculionidae)

The Apennine Mountains in Italy are an important biogeographical region and of particular interest in phylogeographical research, because they have been a refugium during Pleistocene glaciation events for numerous European species. We performed a genetic study on the Eurasian bark beetle Pityogenes chalcographus (Linnaeus, 1760), focusing on two Apennine (Italian) and two Central European (Austrian) locations to assess the influence of the Apennines in the evolutionary history of the beetle, particularly during the Pleistocene. We analysed a part of the mitochondrial COI gene and a set of 5470 informative genome-wide markers to understand its biogeography. We found 75 distinct mitochondrial haplotypes, which are structured in three main clades. In general, the Apennine locations harbour a higher number of mitochondrial clades than Central European sites, with one specific clade exclusively detected in the Apennines. Analysis of our genome-wide, multi-locus dataset reveals a clustering of P. chalcographus by geography, with Italian individuals clearly separated from Austrian samples. Our data highlight the significance of the Apennines for the genetic diversity of P. chalcographus and support the hypothesis that this area was an important refugium during unfavourable conditions in the Pleistocene. We discuss additional life-history traits and processes that shaped the evolution of this widespread beetle.

Shallow Genetic Structure among the European Populations of the Six-Toothed Bark Beetle Ips sexdentatus (Coleoptera, Curculionidae, Scolytinae)

The six-toothed bark beetle, Ips sexdentatus, is one of the most abundant scolytid species of the central and southern European countries. It mostly feeds on Pinus sp., whereas during population outbreaks it can also attack Picea sp. In spite of its broad distribution, its phylogeography has never been studied before. To do that, we employed an mtDNA marker on 489 individuals that covered most of its native range in Europe. Geographic distribution of the 86 haplotypes showed that at least three glacial refugia have played a significant role in shaping the currently observed pattern of genetic divergence in Europe, without excluding the contribution of minor refugial areas that acted in a similar manner. The revealed shallow structure can be considered an artifact of factors that reduced intraspecific diversity, at the same time favoring gene flow. As such, biological traits of the species itself (flying ability and host preference) and even human-mediated transport of wood seem to be the most prevailing and probable reasons that gave rise to the observed pattern.

Pleistocene climate cycling and host plant association shaped the demographic history of the bark beetle Pityogenes chalcographus

Historical climatic oscillations and co-evolutionary dependencies were key evolutionary drivers shaping the current population structure of numerous organisms. Here, we present a genome-wide study on the biogeography of the bark beetle Pityogenes chalcographus, a common and widespread insect in Eurasia. Using Restriction Associated DNA Sequencing, we studied the population structure of this beetle across a wide part of its western Palaearctic range with the goal of elucidating the role of Pleistocene glacial-interglacial cycling and its close relationship to its main host plant Norway spruce. Genetic distance among geographic sites was generally low, but clustering analysis revealed three genetically distinct groups, that is, southern, central/south-eastern, and north-eastern locations. Thus, three key P. chalcographus glacial refugia were identified: in the Italian-Dinaric region, the Carpathians, and the Russian plain, shared with its main host. The current phylogeographic signal was affected by genetic divergence among geographically isolated refugia during glacial periods and postglacial re-establishment of genetic exchange through secondary contact, reflected by admixture among genetic groups. Additionally, certain life history traits, like the beetle’s dispersal and reproductive behaviour, considerably influenced its demographic history. Our results will help to understand the biogeography of other scolytine beetles, especially species with similar life history traits.

Reproductive Manipulators in the Bark Beetle Pityogenes chalcographus (Coleoptera: Curculionidae)-The Role of Cardinium, Rickettsia, Spiroplasma, and Wolbachia

Heritable bacterial endosymbionts can alter the biology of numerous arthropods. They can influence the reproductive outcome of infected hosts, thus affecting the ecology and evolution of various arthropod species. The spruce bark beetle Pityogenes chalcographus (L.) (Coleoptera: Curculionidae: Scolytinae) was reported to express partial, unidirectional crossing incompatibilities among certain European populations. Knowledge on the background of these findings is lacking; however, bacterial endosymbionts have been assumed to manipulate the reproduction of this beetle. Previous work reported low-density and low-frequency Wolbachia infections of P. chalcographus but found it unlikely that this infection results in reproductive alterations. The aim of this study was to test the hypothesis of an endosymbiont-driven incompatibility, other than Wolbachia, reflected by an infection pattern on a wide geographic scale. We performed a polymerase chain reaction (PCR) screening of 226 individuals from 18 European populations for the presence of the endosymbionts Cardinium, Rickettsia, and Spiroplasma, and additionally screened these individuals for Wolbachia. Positive PCR products were sequenced to characterize these bacteria. Our study shows a low prevalence of these four endosymbionts in P. chalcographus. We detected a yet undescribed Spiroplasma strain in a single individual from Greece. This is the first time that this endosymbiont has been found in a bark beetle. Further, Wolbachia was detected in three beetles from two Scandinavian populations and two new Wolbachia strains were described. None of the individuals analyzed were infected with Cardinium and Rickettsia. The low prevalence of bacteria found here does not support the hypothesis of an endosymbiont-driven reproductive incompatibility in P. chalcographus.

A new species of the paper wasp genus Polistes (Hymenoptera, Vespidae, Polistinae) in Europe revealed by morphometrics and molecular analyses

We combine multivariate ratio analysis (MRA) of body measurements and analyses of mitochondrial and nuclear data to examine the status of several species of European paper wasps (Polistes Latreille, 1802) closely related to P. gallicus. Our analyses unambiguously reveal the presence of a cryptic species in Europe, as two distinct species can be recognized in what has hitherto been considered Polistes bischoffi Weyrauch, 1937. One species is almost as light coloured as P. gallicus, and is mainly recorded from Southern Europe and Western Asia. The other species is darker and has a more northern distribution in Central Europe. Both species occur syntopically in Switzerland. Given that the lost lectotype of P. bischoffi originated from Sardinia, we selected a female of the southern species as a neotype. The northern species is described as P. helveticussp. n. here. We also provide a redescription of P. bischoffirev. stat. and an identification key including three more closely related species, P. biglumis, P. gallicus and P. hellenicus.

Divergent evolutionary histories of two sympatric spruce bark beetle species

Ips typographus and Pityogenes chalcographus are two sympatric Palearctic bark beetle species with wide distribution ranges. As both species are comparable in biology, life history, and habitat, including sharing the same host, Picea abies, they provide excellent models for applying a comparative approach in which to identify common historical patterns of population differentiation and the influence of species-specific ecological characteristics. We analysed patterns of genetic diversity, genetic structure and demographic history of ten I. typographus and P. chalcographus populations co-distributed across Europe using both COI and ITS2 markers. Rather than similarities, our results revealed striking differences. Ips typographus was characterised by low genetic diversity, shallow population structure and strong evidence that all extant haplogroups arose via a single Holocene population expansion event. In contrast, genetic variation and structuring were high in P. chalcographus indicating a longer and more complex evolutionary history. This was estimated to be five times older than I. typographus, beginning during the last Pleistocene glacial maximum over 100 000 years ago. Although the expansions of P. chalcographus haplogroups also date to the Holocene or just prior to its onset, we show that these occurred from at least three geographically separated glacial refugia. Overall, these results suggest that the much longer evolutionary history of P. chalcographus greatly influenced the levels of phylogeographic subdivision among lineages and may have led to the evolution of different life-history traits which in turn have affected genetic structure and resulted in an advantage over the more aggressive I. typographus.

Deep sympatric mtDNA divergence in the autumnal moth (Epirrita autumnata)

Deep sympatric intraspecific divergence in mtDNA may reflect cryptic species or formerly distinct lineages in the process of remerging. Preliminary results from DNA barcoding of Scandinavian butterflies and moths showed high intraspecific sequence variation in the autumnal moth, Epirrita autumnata. In this study, specimens from different localities in Norway and some samples from Finland and Scotland, with two congeneric species as outgroups, were sequenced with mitochondrial and nuclear markers to resolve the discrepancy found between mtDNA divergence and present species-level taxonomy. We found five COI sub-clades within the E. autumnata complex, most of which were sympatric and with little geographic structure. Nuclear markers (ITS2 and Wingless) showed little variation and gave no indications that E. autumnata comprises more than one species. The samples were screened with primers for Wolbachia outer surface gene (wsp) and 12% of the samples tested positive. Two Wolbachia strains were associated with different mtDNA sub-clades within E. autumnata, which may indicate indirect selection/selective sweeps on haplotypes. Our results demonstrate that deep mtDNA divergences are not synonymous with cryptic speciation and this has important implications for the use of mtDNA in species delimitation, like in DNA barcoding.

What is Next in Bark Beetle Phylogeography?

Bark beetle species within the scolytid genera Dendroctonus, Ips, Pityogenes and Tomicus are known to cause extensive ecological and economical damage in spruce and pine forests during epidemic outbreaks all around the world. Dendroctonus ponderosae poses the most recent example having destroyed almost 100,000 km² of conifer forests in North America. The success and effectiveness of scolytid species lies mostly in strategies developed over the course of time. Among these, a complex system of semiochemicals promotes the communication and aggregation on the spot of infestation facilitating an en masse attack against a host tree's defenses; or an association with fungi that evolved either in the form of nutrition (ambrosia fungi) or even by reducing the resistance of host trees (blue-stain fungi). Although often specific to a tree genus or species, some bark beetles are polyphagous and have the ability to switch on to new hosts and extend their host range (i.e., between conifer genera such as Pityogenes chalcographus or even from conifer to deciduous trees as Polygraphus grandiclava). A combination of these capabilities in concert with life history or ecological traits explains why bark beetles are considered interesting subjects in evolutionary studies. Several bark beetle species appear in phylogeographic investigations, in an effort to improve our understanding of their ecology, epidemiology and evolution. In this paper investigations that unveil the phylogeographic history of bark beetles are reviewed. A close association between refugial areas and postglacial migration routes that insects and host trees have followed in the last 15,000 BP has been suggested in many studies. Finally, a future perspective of how next generation sequencing will influence the resolution of phylogeographic patterns in the coming years is presented. Utilization of such novel techniques will provide a more detailed insight into the genome of scolytids facilitating at the same time the application of neutral and non-neutral markers. The latter markers in particular promise to enhance the study of eco-physiological reaction types like the so-called pioneer beetles or obligate diapausing individuals.

Avtzis D, Riegler M, Stauffer C. Mitochondrial phylogenies in the light of pseudogenes and Wolbachia: re-assessment of a bark beetle dataset

Phylogenetic studies based on mtDNA become increasingly questioned because of potential pitfalls due to mitochondrial pseudogenes and mitochondrial selective sweeps. While the inclusion of nuclear markers should preferentially be considered for future studies, there is no need to abandon mtDNA as long as tests for the known mtDNA artefacts are performed. In this study we presentadditionaldata and test previous phylogeographical studies of Pityogenes chalcographus. We did not detect nuclear copies (numts) of the previously used mitochondrial markers by performing a combined long range/nested PCR of the COI gene and by an in silico analysis of the COI sequence data. This confirms the robustness of our previous phylogenetic study of Pityogenes chalcographus. Results of an in-situ hybridization of Wolbachia in Pityogenes chalcographus confirm the presence of this endosysmbiont in this species. However, we did not detect a correlation between infection status, geographical region and mtDNA haplotypes. The hybridisation data also support a previous hypothesis that infections do not result from parasitoids or parasitic nematodes, insect surface or laboratory contaminations and are hence a true infection of Pityogenes chalcographus. We conclude that the deep structure found in mitochondrial populations of Pityogenes chalcographus indeed represents the evolutionary history of European populations.

Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration

Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My(-1) for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.

Genetic structure of Japanese populations of Xylosandrus brevis (Curculionidae: Scolytinae)

We examined the genetic structure of populations of an ambrosia beetle, Xylosandrus brevis (Eichhoff) (Curculionidae: Scolytinae), to understand its colonization dynamics. We collected specimens from 20 sites in Japan and studied the genetic structure of these populations using portions of the mitochondrial cytochrome oxidase I gene (COI). A phylogenetic analysis showed three distinct lineages (clades A, B, and C) within X. brevis. Clade A had 65 haplotypes from all the populations, except for populations from Nagano (Chiisagata-gun) and the Ryukyu Islands (Ishigaki), whereas clade B had 14 haplotypes from nine populations (Yamagata, Saitama, Shimo-Minochi-gun, Chiisagata-gun, Toyota, Watarai-gun, Wakayama, Tottori, and Kochi), and clade C had 6 haplotypes from the Ryukyu Islands (Ishigaki) population (and nowhere else). Nested clade phylogeographic analysis showed 65 clade A haplotypes and 14 clade B haplotypes geographically structured in two clades, respectively. A contact zone was identified in the Chubu and Tokai areas. Our results suggest that gene flow and individual movement of X. brevis between the Ryukyu Islands and the other three main islands of Japan has been rare, and X. brevis may be divided into two populations, eastern-central and northern-western, with little gene flow between the four areas of western Japan (Kinki, Chugoku, Shikoku, and Kyushu).

Complex postglacial history of the temperate bark beetle Tomicus piniperda L. (Coleoptera, Scolytinae)

Tomicus piniperda is an economically important pine bark beetle infesting European Pinus spp. stands. We sequenced and analyzed 797 bp of the mitochondrial genome from individuals obtained from 34 populations sampled throughout the European range. We obtained 36 haplotypes, from which a haplotype network was constructed. In the Iberian Peninsula, high-genetic variability was detected with numerous endemic haplotypes. In contrast, the other European populations were less diverse with a single haplotype predominating from the Pyrenees to Scandinavia. Nevertheless, even within Europe, a few populations showed significant amounts of diversity. Four groups were obtained by Spatial Analysis of Molecular Variance, illustrating the regional characteristics of the species. T. piniperda had multiple fragmented refugia in the Iberian Peninsula. These currently isolated populations only partly contributed to postglacial re-colonizations of Northern Europe during interglacials. Nevertheless, few long-range migration events up to Northern Europe were detected, mostly originating from the Pyrenees. In the rest of Europe, the phylogeographical patterns were unclear, because of repeated cycles of contraction and expansion. The genetic analysis showed one glacial refugium in North-Central Europe, whereas other refugia most likely occurred in the Southern Alps, Apennine and the Balkans. The phylogeographical pattern depicted here reflects partly the postglacial history of the beetles' main host tree P. sylvestris.

Evidence for low-titre infections in insect symbiosis: Wolbachia in the bark beetle Pityogenes chalcographus (Coleoptera, Scolytinae)

Wolbachia are obligatory endosymbiotic alpha-proteobacteria found in many insect species. They are maternally transmitted and often exhibit reproductive phenotypes like cytoplasmic incompatibility. Pityogenes chalcographus is a bark beetle causing severe damage in spruce stands. Its European populations are divided into several mitochondrial clades separated by partial crossing barriers. In this study, we tested a large sample set covering the natural range of the beetle in Europe for the presence of Wolbachia and associations between infection pattern and mitotypes using a highly sensitive nested PCR technique. 35.5% of the individuals were infected with the endosymbiont and two distinct strains were identified. Both strains occur in low titre not accessible by conventional detection methods. The infections are present all over Europe, unlikely to cause the partial crossing barriers in this host and uncoupled from mitochondrial clades. This pattern is indicative for populations evolving towards endosymbiont loss and for repeated intraspecific horizontal transfer of Wolbachia. Alternatively, the low-titre infections found in P. chalcographus are yet another example for Wolbachia that can persist in host species at low densities and frequencies.