Divergent evolutionary histories of two sympatric spruce bark beetle species

Complex Genomic Landscape of Inversion Polymorphism in Europe's Most Destructive Forest Pest

In many species, polymorphic genomic inversions underlie complex phenotypic polymorphisms and facilitate local adaptation in the face of gene flow. Multiple polymorphic inversions can co-occur in a genome, but the prevalence, evolutionary significance, and limits to complexity of genomic inversion landscapes remain poorly understood. Here, we examine genome-wide genetic variation in one of Europe's most destructive forest pests, the spruce bark beetle Ips typographus, scan for polymorphic inversions, and test whether inversions are associated with key traits in this species. We analyzed 240 individuals from 18 populations across the species' European range and, using a whole-genome resequencing approach, identified 27 polymorphic inversions covering ∼28% of the genome. The inversions vary in size and in levels of intra-inversion recombination, are highly polymorphic across the species range, and often overlap, forming a complex genomic architecture. We found no support for mechanisms such as directional selection, overdominance, and associative overdominance that are often invoked to explain the presence of large inversion polymorphisms in the genome. This suggests that inversions are either neutral or maintained by the combined action of multiple evolutionary forces. We also found that inversions are enriched in odorant receptor genes encoding elements of recognition pathways for host plants, mates, and symbiotic fungi. Our results indicate that the genome of this major forest pest of growing social, political, and economic importance harbors one of the most complex inversion landscapes described to date and raise questions about the limits of intraspecific genomic architecture complexity.

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.

Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden

The Eurasian spruce bark beetle, Ips typographus, is a major pest, capable of killing spruce forests during large population outbreaks. Recorded dispersal distances of individual beetles are typically within hundreds of meters or a few kilometers. However, the connectivity between populations at larger distances and longer time spans and how this is affected by the habitat is less studied, despite its importance for understanding at which distances local outbreaks may spread. Previous population genetic studies in I. typographus typically used low resolution markers. Here, we use genome-wide data to assess population structure and connectivity of I. typographus in Sweden. We used 152 individuals from 19 population samples, distributed over 830 km from Strömsund (63° 46' 8″ N) in the north to Nyteboda (56° 8' 50″ N) in the south, to capture processes at a large regional scale, and a transect sampling design adjacent to a recent outbreak to capture processes at a smaller scale (76 km). Using restriction site-associated DNA sequencing (RADseq) markers capturing 1409-1997 SNPs throughout the genome, we document a weak genetic structure over the large scale, potentially indicative of high connectivity with extensive gene flow. No differentiation was detected at the smaller scale. We find indications of isolation-by-distance both for relative (F ST) and absolute divergence (Dxy). The two northernmost populations are most differentiated from the remaining populations, and diverge in parallel to the southern populations for a set of outlier loci. In conclusion, the population structure of I. typographus in Sweden is weak, suggesting a high capacity to disperse and establish outbreak populations in new territories.

Insights into the Divergence of Chinese Ips Bark Beetles during Evolutionary Adaptation

Simple Summary

Bark beetle species of the genus Ips are among the major pests of Chinese conifer forests. Based on mitochondrial genome and SNP, we investigated the phylogenetic relationships and evolutionary trends of 19 populations of six Ips species that had serious outbreaks in recent years. Our results demonstrated the relationships between Ips evolution and host plants, pheromones, and altitudinal differences, and provided new insights into the mechanism of adaptive evolution of Ips bark beetles.

Abstract

Many bark beetles of the genus Ips are economically important insect pests that cause severe damage to conifer forests worldwide. In this study, sequencing the mitochondrial genome and restriction site-associated DNA of Ips bark beetles helps us understand their phylogenetic relationships, biogeographic history, and evolution of ecological traits (e.g., pheromones and host plants). Our results show that the same topology in phylogenetic trees constructed in different ways (ML/MP/BI) and with different data (mtDNA/SNP) helps us to clarify the phylogenetic relationships between Chinese Ips bark beetle populations and Euramerican species and their higher order clades; Ips bark beetles are polyphyletic. The structure of the mitochondrial genome of Ips bark beetles is similar and conserved to some extent, especially in the sibling species Ips typographus and Ips nitidus. Genetic differences among Ips species are mainly related to their geographic distribution and different hosts. The evolutionary pattern of aggregation pheromones of Ips species reflects their adaptations to the environment and differences among hosts in their evolutionary process. The evolution of Ips species is closely related to the uplift of the Qinghai-Tibet Plateau and host switching. Our study addresses the evolutionary trend and phylogenetic relationships of Ips bark beetles in China, and also provides a new perspective on the evolution of bark beetles and their relationships with host plants and pheromones.

Genotyping by sequencing reveals lack of local genetic structure between two German Ips typographus L. populations

The European spruce bark beetle (Ips typographus L.) is a serious pest in Norway spruce stands. While usually attacking freshly fallen trees or trees with a reduced defense system, also healthy trees can be infested during massive outbreaks of I. typographus that can occur after catastrophic events such as drought periods or storms. Knowledge of the genetic structure of this species, especially on local scales is still ambiguous. While local population structure was reported in some studies, others did not detect any differentiation among I. typographus populations. Here, we used genotyping by sequencing to infer the genetic structure of two I. typographus populations in western Germany, which had a distance of approx. 58 km from each other. Based on 16,830 SNPs we detected high genetic diversity, but very low genetic differentiation between the populations (FST: 0.001) and a lack of population structure. These results suggest a high dispersal ability of I. typographus.

Studying genetic population structure to shed light on the demographic explosion of the rare species Barbitistes vicetinus (Orthoptera, Tettigoniidae)

Insect outbreaks usually involve important ecological and economic consequences for agriculture and forestry. The short-winged bush-cricket Barbitistes vicetinus Galvagni & Fontana, 1993 is a recently described species that was considered rare until ten years ago, when unexpected population outbreaks causing severe defoliations across forests and crops were observed in north-eastern Italy. A genetic approach was used to analyse the origin of outbreak populations. The analysis of two mitochondrial regions (Cytochrome Oxidase I and II and 12S rRNA-Control Region) of 130 samples from the two disjunct ranges (Euganean and Berici Hills) showed high values of haplotype diversity and revealed a high geographical structure among populations of the two ranges. The high genetic variability observed supports the native origin of this species. In addition, results suggest that unexpected outbreaks are not a consequence of a single or few pestiferous haplotypes but rather the source of outbreaks are local populations which have experienced an increase in each area. The recent outbreaks have probably appeared independently of the genetic haplotypes whereas environmental conditions could have affected the outbreak populations. These findings contribute to a growing understanding of the status and evolutionary history of the pest that would be useful for developing and implementing biological control strategies for example by maximizing efforts to locate native natural enemies.

Climatic oscillations in Quaternary have shaped the co-evolutionary patterns between the Norway spruce and its host-associated herbivore

During the Last Glacial Maximum in the Northern Hemisphere, expanding ice sheets forced a large number of plants, including trees, to retreat from their primary distribution areas. Many host-associated herbivores migrated along with their host plants. Long-lasting geographic isolation between glacial refugia could have been led to the allopatric speciation in separated populations. Here, we have studied whether the migration history of the Norway spruce Picea abies in Quaternary has affected its host-associated herbivorous beetle—Monochamus sartor. By using microsatellite markers accompanied by the geometric morphometrics analysis of wing venation, we have revealed the clear geographic structure of M. sartor in Eurasia, encompassing two main clusters: southern (Alpine–Carpathian) and eastern (including northeastern Europe and Asia), which reflects the northern and southern ecotypes of its host. The two beetles’ lineages probably diverged during the Pleniglacial (57,000—15,000 BC) when their host tree species was undergoing significant range fragmentation and experienced secondary contact during post-glacial recolonization of spruce in the Holocene. A secondary contact of divergent lineages of M. sartor has resulted in the formation of the hybrid zone in northeastern Europe. Our findings suggest that the climatic oscillations during the Pleistocene have driven an insect-plant co-evolutionary process, and have contributed to the formation of the unique biodiversity of Europe.

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.

Population genetic structure and assessment of allochronic divergence in the Macoun’s Arctic (Oeneis macounii) butterfly

Patterns in the genetic variation of species can be used to infer their specific demographic and evolutionary history and provide insight into the general mechanisms underlying population divergence and speciation. The Macoun’s Arctic (Oeneis macounii (W.H. Edwards, 1885); MA) butterfly occurs across Canada and parts of the northern United States in association with jack pine (Pinus banksiana Lamb.) and lodgepole pine (Pinus contorta Douglas ex Loudon). MA’s current distribution is highly fragmented, and the extent of reproductive isolation among allopatric populations is unknown. Furthermore, although MA is biennial, adults emerge every year in some populations. These populations presumably consist of two alternate-year cohorts, providing the opportunity for sympatric divergence via allochronic isolation. Using mitochondrial DNA (mtDNA) and amplified fragment length polymorphism (AFLP) markers, we analyzed MA’s genetic structure to determine the current and historical role of allopatric and allochronic isolation in MA population divergence. Both markers revealed high diversity and a low, but significant, degree of spatial structure and pattern of isolation by distance. Phylogeographic structure was generally absent, with low divergence among mtDNA haplotypes. MA likely exhibits low dispersal and gene flow among most allopatric populations; however, there was no evidence of differentiation resulting from allochronic isolation for sympatric cohorts.

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.

Ophiostomatoid fungi associated with the spruce bark beetle Ips typographus, including 11 new species from China

Ips typographus (Coleoptera, Scolytinae) is a spruce-infesting bark beetle that occurs throughout Europe and Asia. The beetle can cause considerable damage, especially when colonized trees are stressed and beetle populations increase. Although some studies have shown that populations of I. typographus in Europe, China and Japan are genetically distinct, these populations are biologically similar, including a strong association with ophiostomatoid fungi. To date, only two Leptographium spp. have been reported from the beetle in China, while 40 species have been reported from Europe and 13 from Japan. The aims of this study were to identify the ophiostomatoid fungal associates of I. typographus in north-eastern China, and to determine whether the fungal assemblages reflect the different geographical populations of the beetle. Field surveys in Jilin and Heilongjiang provinces yielded a total of 1 046 fungal isolates from 145 beetles and 178 galleries. Isolates were grouped based on morphology and representatives of each group were identified using DNA sequences of the ribosomal LSU, ITS, β-tubulin, calmodulin and elongation factor 1-α gene regions. A total of 23 species of ophiostomatoid fungi were identified, including 12 previously described species and 11 novel species, all of which are described here. The dominant species were Ophiostoma bicolor, Leptographium taigense and Grosmannia piceiperda D, representing 40.5 %, 27.8 % and 17.8 % of the isolates, respectively. Comparisons of species from China, Europe and Japan are complicated by the fact that some of the European and all the Japanese species were identified based only on morphology. However, assuming that those identifications are correct, five species were shared between Europe, Japan and China, two species were shared between China and Japan, five between Europe and China, and two between Europe and Japan. Consequently, Ips typographus populations in these different geographic areas have different fungal assemblages, suggesting that the majority of these beetle-associations are promiscuous. The results also suggested that the symbionts of the bark beetle do not reflect the population structures of the beetle. The use of fungal symbiont assemblages to infer population structures and invasion history of its vectors should thus be interpreted with circumspection.

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.

Phylogeography of the Wheat Stem Sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae): Implications for Pest Management

The wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), is a key pest of wheat in the northern Great Plains of North America, and damage resulting from this species has recently expanded southward. Current pest management practices are inadequate and uncertainty regarding geographic origin, as well as limited data on population structure and dynamics across North America impede progress towards more informed management. We examined the genetic divergence between samples collected in North America and northeastern Asia, the assumed native range of C. cinctus using two mitochondrial regions (COI and 16S). Subsequently, we characterized the structure of genetic diversity in the main wheat producing areas in North America using a combination of mtDNA marker and microsatellites in samples collected both in wheat fields and in grasses in wildlands. The strong genetic divergence observed between North American samples and Asian congeners, in particular the synonimized C. hyalinatus, did not support the hypothesis of a recent American colonization by C. cinctus. Furthermore, the relatively high genetic diversity both with mtDNA and microsatellite markers offered additional evidence in favor of the native American origin of this pest. The genetic diversity of North American populations is structured into three genetic clusters and these are highly correlated with geography. Regarding the recent southern outbreaks in North America, the results tend to exclude the hypothesis of recent movement of damaging wheat stem sawfly populations from the northern area. The shift in host plant use by local populations appears to be the most likely scenario. Finally, the significance of these findings is discussed in the context of pest management.

Late Glacial Demographic Expansion Motivates a Clock Overhaul for Population Genetics

The molecular clock hypothesis is fundamental in evolutionary biology as by assuming constancy of the molecular rate it provides a timeframe for evolution. However, increasing evidence shows time dependence of inferred molecular rates with inflated values obtained using recent calibrations. As recent demographic calibrations are virtually non-existent in most species, older phylogenetic calibration points (>1 Ma) are commonly used, which overestimate demographic parameters. To obtain more reliable rates of molecular evolution for population studies, I propose the calibration of demographic transition (CDT) method, which uses the timing of climatic changes over the late glacial warming period to calibrate expansions in various species. Simulation approaches and empirical data sets from a diversity of species (from mollusk to humans) confirm that, when compared with other genealogy-based calibration methods, the CDT provides a robust and broadly applicable clock for population genetics. The resulting CDT rates of molecular evolution also confirm rate heterogeneity over time and among taxa. Comparisons of expansion dates with ecological evidence confirm the inaccuracy of phylogenetically derived divergence rates when dating population-level events. The CDT method opens opportunities for addressing issues such as demographic responses to past climate change and the origin of rate heterogeneity related to taxa, genes, time, and genetic information content.

Genetic diversity of Thaumetopoea pityocampa in Greece: the role of Quaternary changes in Aegean Sea

Thaumetopoea pityocampa, the winter pine processionary moth, is one of the most important pests of pine trees in the Mediterranean region. To learn more about the refugial areas within the greater refugium of Greece, samples from 15 local populations were collected. Analysis of the Cytochrome Oxidase I region identified 15 haplotypes. One strongly supported clade was found, separating the Aegean island of Lesvos from the mainland populations. Mdiv analysis showed that this clade diverged from the general clade 155,000 y.a., suggesting the sea level changes during the Quaternary Period as a possible reason for its seclusion. Additionally, comparisons with similar studies in this region revealed a possible colonization of the eastern Aegean islands from the Turkish mainland rather than from Greece. However, no strong isolation-by-distance events were detected among the mainland populations, which could be attributed to the joint effect of regular gene flow and the lack of insurmountable geographic barriers. Finally, regarding population structure, Bayesian analysis as well as neutrality tests pointed towards an ongoing population expansion which verifies the potential invasiveness of this pest species, something that will have to be dealt with under the influence of climate change.

Comparative multilocus phylogeography of two Palaearctic spruce bark beetles: influence of contrasting ecological strategies on genetic variation

While phylogeographic patterns of organisms are often interpreted through past environmental disturbances, mediated by climate changes, and geographic barriers, they may also be strongly influenced by species-specific traits. To investigate the impact of such traits, we focused on two Eurasian spruce bark beetles that share a similar geographic distribution, but differ in their ecology and reproduction. Ips typographus is an aggressive tree-killing species characterized by strong dispersal, whereas Dendroctonus micans is a discrete inbreeding species (sib mating is the rule), parasite of living trees and a poor disperser. We compared genetic variation between the two species over both beetles' entire range in Eurasia with five independent gene fragments, to evaluate whether their intrinsic differences could have an influence over their phylogeographic patterns. We highlighted widely divergent patterns of genetic variation for the two species and argue that the difference is indeed largely compatible with their contrasting dispersal strategies and modes of reproduction. In addition, genetic structure in I. typographus divides European populations in a northern and a southern group, as was previously observed for its host plant, and suggests past allopatric divergence. A long divergence time was estimated between East Asian and other populations of both species, indicating their long-standing presence in Eurasia, prior to the last glacial maximum. Finally, the strong population structure observed in D. micans for the mitochondrial locus provides insights into the recent colonization history of this species, from its native European range to regions where it was recently introduced.

Temporal population genetic instability in range-edge western toads, Anaxyrus boreas

In this article, we address the temporal stability of population genetic structure in a range-edge population that is undergoing continual, short-distance colonization events. We sampled western toad, Anaxyrus boreas, breeding populations over 2 seasons near their northern range limit in southeast Alaska. We sampled 20 ponds each during the summers of 2008 and 2009, with 14 ponds sampled in both summers. We found considerable turnover in the population genetic relationships among ponds in those 2 seasons, as well as biologically meaningful genetic differentiation between years within some ponds. We found relatively consistent relationships between major population centers, whereas the relationships between the central ponds and smaller, outlying populations differed year to year. This finding indicates that multiple years of genetic sampling may be important for understanding the genetic landscape of some populations.