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

Signature of mid-Pleistocene lineages in the European silver fir (Abies alba Mill.) at its geographic distribution margin

In a conservation and sustainable management perspective, we identify the ecological, climatic, and demographic factors responsible for the genetic diversity patterns of the European silver fir (Abies alba Mill.) at its southwestern range margin (Pyrenees Mountains, France, Europe). We sampled 45 populations throughout the French Pyrenees and eight neighboring reference populations in the Massif Central, Alps, and Corsica. We genotyped 1,620 individuals at three chloroplast and ten nuclear microsatellite loci. We analyzed within- and among-population genetic diversity using phylogeographic reconstructions, tests of isolation-by-distance, Bayesian population structure inference, modeling of demographic scenarios, and regression analyses of genetic variables with current and past environmental variables. Genetic diversity decreased from east to west suggesting isolation-by-distance from the Alps to the Pyrenees and from the Eastern to the Western Pyrenees. We identified two Pyrenean lineages that diverged from a third Alpine-Corsica-Massif Central lineage 0.8 to 1.1 M years ago and subsequently formed a secondary contact zone in the Central Pyrenees. Population sizes underwent contrasted changes, with a contraction in the west and an expansion in the east. Glacial climate affected the genetic composition of the populations, with the western genetic cluster only observed in locations corresponding to the coldest past climate and highest elevations. The eastern cluster was observed over a larger range of temperatures and elevations. All demographic events shaping the current spatial structure of genetic diversity took place during the Mid-Pleistocene Transition, long before the onset of the Holocene. The Western Pyrenees lineage may require additional conservation efforts, whereas the eastern lineage is well protected in in situ gene conservation units. Due to past climate oscillations and the likely emergence of independent refugia, east-west oriented mountain ranges may be important reservoir of genetic diversity in a context of past and ongoing climate change in Europe.

Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles

Bark beetles are feared as pests in forestry but they also support a large number of other taxa that exploit the beetles and their galleries. Among arthropods, mites are the largest taxon associated with bark beetles. Many of these mites are phoretic and often involved in complex interactions with the beetles and other organisms. Within the oribatid mite family Scheloribatidae, only two of the three nominal species of Paraleius have been frequently found in galleries of bark beetles and on the beetles themselves. One of the species, P. leontonychus, has a wide distribution range spanning over three ecozones of the world and is believed to be a host generalist, reported from numerous bark beetle and tree species. In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. Moreover, mito-nuclear discordance indicates a case of past hybridization/introgression among distinct Paraleius species, the first case of interspecific hybridization reported in mites other than ticks.

From refugia to contact: Pine processionary moth hybrid zone in a complex biogeographic setting

Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here, we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyze their co-occurrence and hybridization patterns in this biogeographic context. We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between markers and complementary assignment methods to identify and map hybrids and parental individuals. We confirmed the parapatric distribution of Thaumetopoea pityocampa (Lepidoptera: Notodontidae) in the west and Thaumetopoea wilkinsoni in the east and identified a narrow contact zone. We identified several glacial refugia of T. wilkinsoni in southern Turkey with a strong east-west differentiation in this species. Unexpectedly, T. pityocampa crossed the TSS and occur in northern Aegean Turkey and some eastern Greek islands. We found robust evidence of introgression between the two species in a restricted zone in northwestern Turkey, but we did not identify any F1 individuals. The identified hybrid zone was mostly bimodal. The distributions and genetic patterns of the studied species were strongly influenced both by the Quaternary climatic oscillations and the complex geological history of the Aegean region. T. pityocampa and T. wilkinsoni survived the last glacial maximum in disjoint refugia and met in western Turkey at the edge of the recolonization routes. Expanding population of T. wilkinsoni constrained T. pityocampa to the western Turkish shore. Additionally, we found evidence of recurrent introgression by T. wilkinsoni males in several T. pityocampa populations. Our results suggest that some prezygotic isolation mechanisms, such as differences in timing of the adult emergences, might be a driver of the isolation between the sister species.

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.

Analysis of the population structure of Macrolophus pygmaeus (Rambur) (Hemiptera: Miridae) in the Palaearctic region using microsatellite markers

Macrolophus pygmaeus (Rambur) (Hemiptera: Miridae) is widely distributed throughout the Palaearctic region. The aim was to explain the current geographic distribution of the species by investigating its genetic population structure. Samples of M. pygmaeus were collected in 15 localities through its range of distribution. A sample from a commercial producer was also analyzed. A total of 367 M. pygmaeus were genotyped for nine microsatellite loci. Isolation by distance was tested by Mantel's test. The molecular structure of M. pygmaeus populations was inferred by UPGMA, AMOVA, Principal component and Bayesian analyses. The average number of alleles per locus per population was 5.5 (range: 3.1–7.8). Istanbul (Turkey) and Nimes (France) had the lowest (0.291) and the highest (0.626) expected heterozygosity (H_e), respectively. There was an increase in H_e from the Canary Islands to Nimes, and a progressive decrease thereafter. A significant negative correlation was found between allelic richness and H_e, and the distance of each population to the easternmost locality (Canary Islands). Significant linkage disequilibrium was observed in the populations from Turkey. F_ST (0.004–0.334) indicated a high population differentiation, with isolation by distance supported by a high correlation. Bayesian analyses, PCA, and UPGMA pointed to three main clusters: (1) Greece and Turkey, (2) Italy and France, and (3) southern Iberia and the Canary Islands. The recent evolutionary history of M. pygmaeus is inferred from the data as follows: (1) the reduction in the geographic distribution of the species to the Iberian, Italian, and Balkan peninsulas, and possibly southern France, during glaciations and re-colonization of northern Europe from its southern refuges; (2) the maintenance of high diversity in Iberia and Italy (and possibly southern France) during contraction periods, and bottlenecks in the Balkans; (3) introgression of the Italian–French lineage in northern Spain, naturally or through trade.

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.

Global transcriptome profiling of the pine shoot beetle, Tomicus yunnanensis (Coleoptera: Scolytinae)

Background

The pine shoot beetle Tomicus yunnanensis (Coleoptera: Scolytinae) is an economically important pest of Pinus yunnanensis in southwestern China. Developed resistance to insecticides due to chemical pesticides being used for a long time is a factor involved in its serious damage, which poses a challenge for management. In addition, highly efficient adaptation to divergent environmental ecologies results in this pest posing great potential threat to pine forests. However, the molecular mechanisms remain unknown as only limited nucleotide sequence data for this species is available.

Methodology/Principal Findings

In this study, we applied next generation sequencing (Illumina sequencing) to sequence the adult transcriptome of T. yunnanensis. A total of 51,822,230 reads were obtained. They were assembled into 140,702 scaffolds, and 60,031 unigenes. The unigenes were further functionally annotated with gene descriptions, Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genome (KEGG). In total, 80,932 unigenes were classified into GO, 13,599 unigenes were assigned to COG, and 33,875 unigenes were found in KO categories. A biochemical pathway database containing 219 predicted pathways was also created based on the annotations. In depth analysis of the data revealed a large number of genes related to insecticides resistance and heat shock protein genes associated with environmental stress.

Conclusions/Significance

The results facilitate the investigations of molecular resistance mechanisms to insecticides and environmental stress. This study lays the foundation for future functional genomics studies of important biological questions of this pest.

Population genetic structure and phylogeographical pattern of rice grasshopper, Oxya hyla intricata, across Southeast Asia

The rice grasshopper, Oxya hyla intricata, is a rice pest in Southeast Asia. In this study, population genetic diversity and structure of this Oxya species was examined using both DNA sequences and AFLP technology. The samples of 12 populations were collected from four Southeast Asian countries, among which 175 individuals were analysed using mitochondrial DNA cytochrome c oxidase subunit I (COI) sequences, and 232 individuals were examined using amplified fragment length polymorphisms (AFLP) to test whether the phylogeographical pattern and population genetics of this species are related to past geological events and/or climatic oscillations. No obvious trend of genetic diversity was found along a latitude/longitude gradient among different geographical groups. Phylogenetic analysis indicated three deep monophyletic clades that approximately correspond to three geographical regions separated by high mountains and a deep strait, and TCS analysis also revealed three disconnected networks, suggesting that spatial and temporal separations by vicariance, which were also supported by AMOVA as a source of the molecular variance presented among groups. Gene flow analysis showed that there had been frequent historical gene flow among local populations in different regions, but the networks exhibited no shared haplotype among populations. In conclusion, the past geological events and climatic fluctuations are the most important factor on the phylogeographical structure and genetic patterns of O. hyla intricata in Southeast Asia. Habitat, vegetation, and anthropogenic effect may also contribute to gene flow and introgression of this species. Moreover, temperature, abundant rainfall and a diversity of graminaceous species are beneficial for the migration of O. hyla intricata. High haplotype diversity, deep phylogenetic division, negative Fu's F (s) values and unimodal and multimodal distribution shapes all suggest a complicated demographic expansion pattern of these O. hyla intricata populations, which might have been caused by climatic oscillations during glacial periods in the Quaternary.

Quaternary history and contemporary patterns in a currently expanding species

Background

Quaternary climatic oscillations had dramatic effects on species evolution. In northern latitudes, populations had to survive the coldest periods in refugial areas and recurrently colonized northern regions during interglacials. Such a history usually results in a loss of genetic diversity. Populations that did not experience glaciations, in contrast, probably maintained most of their ancestral genetic diversity. These characteristics dramatically affected the present-day distribution of genetic diversity and may influence the ability of species to cope with the current global changes. We conducted a range-wide study of mitochondrial genetic diversity in the pine processionary moth (Thaumetopoea pityocampa/T. wilkinsoni complex, Notodontidae), a forest pest occurring around the Mediterranean Basin and in southern Europe. This species is responding to the current climate change by rapid natural range expansion and can also be accidentally transported by humans. Our aim was to assess if Quaternary climatic oscillations had a different effect across the species' range and to determine if genetic footprints of contemporary processes can be identified in areas of recent introduction.

Results

We identified three main clades that were spatially structured. In most of Europe, the genetic diversity pattern was typical for species that experienced marked glaciation cycles. Except in refugia, European populations were characterized by the occurrence of one main haplotype and by a strong reduction in genetic diversity, which is expected in regions that were rapidly re-colonized when climatic conditions improved. In contrast, all other sub-clades around the Mediterranean Basin occurred in limited parts of the range and were strongly structured in space, as is expected in regions in which the impact of glaciations was limited. In such places, genetic diversity was retained in most populations, and almost all haplotypes were endemic. This pattern was extreme on remote Mediterranean islands (Crete, Cyprus, Corsica) where highly differentiated, endemic haplotypes were found. Recent introductions were typified by the existence of closely-related haplotypes in geographically distant populations, which is difficult to detect in most of Europe because of a lack of overall genetic structure.

Conclusion

In regions that were not prone to marked glaciations, recent moth introductions/expansions could be detected due to the existence of a strong spatial genetic structure. In contrast, in regions that experienced the most intense Quaternary climatic oscillations, the natural populations are not genetically structured, and contemporary patterns of population expansion remain undetected.