Multiple evolutionary origins lead to diversity in the metabolic profiles of ambrosia fungi

Ambrosia fungi are an ecological assemblage cultivated by ambrosia beetles as required nutrient sources. This mutualism evolved in multiple beetle and fungus lineages. Whether convergence in ecology led to convergent metabolism in ambrosia fungi is unknown. We compared the assimilation of 190 carbon sources in five independent pairs of ambrosia fungi and closely related, non-ambrosial species. Ecological convergence versus phylogenetic divergence in carbon source use was tested using variation partitioning. We found no convergence in carbon utilization capacities. Instead, metabolic variation was mostly explained by phylogenetic relationships. In addition, carbon usage in ambrosia fungi was equally diverse as that in non-ambrosial species. Thus, carbon metabolism of each ambrosia fungus is determined by its inherited metabolism, not the transition towards symbiosis. In contrast to other fungus-farming systems of termites and attine ants, the fungal symbionts of ambrosia beetles are functionally diverse, reflecting their independent evolutionary origins.     

Broadscale Specificity in a Bark Beetle–Fungal Symbiosis: a Spatio-temporal Analysis of the Mycangial Fungi of the Western Pine Beetle

Whether and how mutualisms are maintained through ecological and evolutionary time is a seldom studied aspect of bark beetle–fungal symbioses. All bark beetles are associated with fungi and some species have evolved structures for transporting their symbiotic partners. However, the fungal assemblages and specificity in these symbioses are not well known. To determine the distribution of fungi associated with the mycangia of the western pine beetle (Dendroctonus brevicomis), we collected beetles from across the insect’s geographic range including multiple genetically distinct populations. Two fungi, Entomocorticium sp. B and Ceratocystiopsis brevicomi, were isolated from the mycangia of beetles from all locations. Repeated sampling at two sites in Montana found that Entomocorticium sp. B was the most prevalent fungus throughout the beetle’s flight season, and that females carrying that fungus were on average larger than females carrying C. brevicomi. We present evidence that throughout the flight season, over broad geographic distances, and among genetically distinct populations of beetle, the western pine beetle is associated with the same two species of fungi. In addition, we provide evidence that one fungal species is associated with larger adult beetles and therefore might provide greater benefit during beetle development. The importance and maintenance of this bark beetle–fungus interaction is discussed.     

Ophiostomatoid fungi isolated from Japanese red pine and their relationships with bark beetles

We isolated ophiostomatoid fungi from bark beetles infesting Pinus densiflora and their galleries at 24 sites in Japan. Twenty-one ophiostomatoid fungi, including species of Ophiostoma, Grosmannia, Ceratocystiopsis, Leptographium, and Pesotum, were identified. Among these, 11 species were either newly recorded in Japan or were previously undescribed species. Some of these fungal species were isolated from several bark beetles, but other species were isolated from only a particular beetle species. Thus, it is suggested that some ophiostomatoid fungi have specific relationships with particular beetle species. In addition, fungus-beetle biplots from redundancy analysis (RDA) summarizing the effects of beetle ecological characteristics suggested that the association patterns between bark beetles and the associated fungi seemed to be related to the niches occupied by the beetles.     

Relationships among wood‐boring beetles,fungi, and the decomposition of forest biomass

A prevailing paradigm in forest ecology is that wood‐boring beetles facilitate wood decay and carbon cycling, but empirical tests have yielded mixed results. We experimentally determined the effects of wood borers on fungal community assembly and wood decay within pine trunks in the southeastern United States. Pine trunks were made either beetle‐accessible or inaccessible. Fungal communities were compared using culturing and high‐throughput amplicon sequencing (HTAS) of DNA and RNA. Prior to beetle infestation, living pines had diverse fungal endophyte communities. Endophytes were displaced by beetle‐associated fungi in beetle‐accessible trees, whereas some endophytes persisted as saprotrophs in beetle‐excluded trees. Beetles increased fungal diversity several fold. Over forty taxa of Ascomycota were significantly associated with beetles, but beetles were not consistently associated with any known wood‐decaying fungi. Instead, increasing ambrosia beetle infestations caused reduced decay, consistent with previous in vitro experiments that showed beetle‐associated fungi reduce decay rates by competing with decay fungi. No effect of bark‐inhabiting beetles on decay was detected. Platypodines carried significantly more fungal taxa than scolytines. Molecular results were validated by synthetic and biological mock communities and were consistent across methodologies. RNA sequencing confirmed that beetle‐associated fungi were biologically active in the wood. Metabarcode sequencing of the LSU/28S marker recovered important fungal symbionts that were missed by ITS2, though community‐level effects were similar between markers. In contrast to the current paradigm, our results indicate ambrosia beetles introduce diverse fungal communities that do not extensively decay wood, but instead reduce decay rates by competing with wood decay fungi.     

REPEATED EVOLUTION OF CROP THEFT IN FUNGUS‐FARMING AMBROSIA BEETLES

Ambrosia beetles, dominant wood degraders in the tropics, create tunnels in dead trees and employ gardens of symbiotic fungi to extract nutrients from wood. Specificity of the beetle–fungus relationship has rarely been examined, and simple vertical transmission of a specific fungal cultivar by each beetle species is often assumed in literature. We report repeated evolution of fungal crop stealing, termed mycocleptism, among ambrosia beetles. The mycocleptic species seek brood galleries of other species, and exploit their established fungal gardens by tunneling through the ambient mycelium‐laden wood. Instead of carrying their own fungal sybmbionts, mycocleptae depend on adopting the fungal assemblages of their host species, as shown by an analysis of fungal DNA from beetle galleries. The evidence for widespread horizontal exchange of fungi between beetles challenges the traditional concept of ambrosia fungi as species‐specific symbionts. Fungus stealing appears to be an evolutionarily successful strategy. It evolved independently in several beetle clades, two of which have radiated, and at least one case was accompanied by a loss of the beetles’ fungus‐transporting organs. We demonstrate this using the first robust phylogeny of one of the world's largest group of ambrosia beetles, Xyleborini.     

Dispersal ability and habitat requirements determine landscape‐level genetic patterns in desert aquatic insects

Species occupying the same geographic range can exhibit remarkably different population structures across the landscape, ranging from highly diversified to panmictic. Given limitations on collecting population‐level data for large numbers of species, ecologists seek to identify proximate organismal traits—such as dispersal ability, habitat preference and life history—that are strong predictors of realized population structure. We examined how dispersal ability and habitat structure affect the regional balance of gene flow and genetic drift within three aquatic insects that represent the range of dispersal abilities and habitat requirements observed in desert stream insect communities. For each species, we tested for linear relationships between genetic distances and geographic distances using Euclidean and landscape‐based metrics of resistance. We found that the moderate‐disperser Mesocapnia arizonensis (Plecoptera: Capniidae) has a strong isolation‐by‐distance pattern, suggesting migration–drift equilibrium. By contrast, population structure in the flightless Abedus herberti (Hemiptera: Belostomatidae) is influenced by genetic drift, while gene flow is the dominant force in the strong‐flying Boreonectes aequinoctialis (Coleoptera: Dytiscidae). The best‐fitting landscape model for M. arizonensis was based on Euclidean distance. Analyses also identified a strong spatial scale‐dependence, where landscape genetic methods only performed well for species that were intermediate in dispersal ability. Our results highlight the fact that when either gene flow or genetic drift dominates in shaping population structure, no detectable relationship between genetic and geographic distances is expected at certain spatial scales. This study provides insight into how gene flow and drift interact at the regional scale for these insects as well as the organisms that share similar habitats and dispersal abilities.     

Experimental evidence of bark beetle adaptation to a fungal symbiont

The importance of symbiotic microbes to insects cannot be overstated; however, we have a poor understanding of the evolutionary processes that shape most insect–microbe interactions. Many bark beetle (Coleoptera: Curculionidae, Scolytinae) species are involved in what have been described as obligate mutualisms with symbiotic fungi. Beetles benefit through supplementing their nutrient‐poor diet with fungi and the fungi benefit through gaining transportation to resources. However, only a few beetle–fungal symbioses have been experimentally manipulated to test whether the relationship is obligate. Furthermore, none have tested for adaptation of beetles to their specific symbionts, one of the requirements for coevolution. We experimentally manipulated the western pine beetle–fungus symbiosis to determine whether the beetle is obligately dependent upon fungi and to test for fine‐scale adaptation of the beetle to one of its symbiotic fungi, Entomocorticium sp. B. We reared beetles from a single population with either a natal isolate of E. sp. B (isolated from the same population from which the beetles originated), a non‐natal isolate (a genetically divergent isolate from a geographically distant beetle population), or with no fungi. We found that fungi were crucial for the successful development of western pine beetles. We also found no significant difference in the effects of the natal and non‐natal isolate on beetle fitness parameters. However, brood adult beetles failed to incorporate the non‐natal fungus into their fungal transport structure (mycangium) indicating adaption by the beetle to particular genotypes of symbiotic fungi. Our results suggest that beetle–fungus mutualisms and symbiont fidelity may be maintained via an undescribed recognition mechanism of the beetles for particular symbionts that may promote particular associations through time.     

Landscape genetics of a pollinator longhorn beetle [Typocerus v. velutinus (Olivier)] on a continuous habitat surface

Landscape connectivity, the degree to which the landscape structure facilitates or impedes organismal movement and gene flow, is increasingly important to conservationists and land managers. Metrics for describing the undulating shape of continuous habitat surfaces can expand the usefulness of continuous gradient surfaces that describe habitat and predict the flow of organisms and genes. We adopted a landscape gradient model of habitat and used surface metrics of connectivity to model the genetic continuity between populations of the banded longhorn beetle [Typocerus v. velutinus (Olivier)] collected at 17 sites across a fragmentation gradient in Indiana, USA. We tested the hypothesis that greater habitat connectivity facilitates gene flow between beetle populations against a null model of isolation by distance (IBD). We used next‐generation sequencing to develop 10 polymorphic microsatellite loci and genotype the individual beetles to assess the population genetic structure. Isolation by distance did not explain the population genetic structure. The surface metrics model of habitat connectivity explained the variance in genetic dissimilarities 30 times better than the IBD model. We conclude that surface metrology of habitat maps is a powerful extension of landscape genetics in heterogeneous landscapes.     

Connectivity in a pond system influences migration and genetic structure in threespine stickleback

Neutral genetic structure of natural populations is primarily influenced by migration (the movement of individuals and, subsequently, their genes) and drift (the statistical chance of losing genetic diversity over time). Migration between populations is influenced by several factors, including individual behavior, physical barriers, and environmental heterogeneity among populations. However, drift is expected to be stronger in populations with low immigration rate and small effective population size. With the technological advancement in geological information systems and spatial analysis tools, landscape genetics now allows the development of realistic migration models and increased insight to important processes influencing diversity of natural populations. In this study, we investigated the relationship between landscape connectivity and genetic distance of threespine stickleback (Gasterosteus aculeatus) inhabiting a pond complex in Belgjarskógur, Northeast Iceland. We used two landscape genetic approaches (i.e., least-cost-path and isolation-by-resistance) and asked whether gene flow, as measured by genetic distance, was more strongly associated with Euclidean distance (isolation-by-distance) or with landscape connectivity provided by areas prone to flooding (as indicated by Carex sp. cover)? We found substantial genetic structure across the study area, with pairwise genetic distances among populations (D_PS) ranging from 0.118 to 0.488. Genetic distances among populations were more strongly correlated with least-cost-path and isolation-by-resistance than with Euclidean distance, whereas the relative contribution of isolation-by-resistance and Euclidian distance could not be disentangled. These results indicate that migration among stickleback populations occurs via periodically flooded areas. Overall, this study highlights the importance of transient landscape elements influencing migration and genetic structure of populations at small spatial scales.     

Environmental drivers of species composition and functional diversity of dung beetles along the Atlantic Forest–Pampa transition zone

Human activities are causing a rapid loss of biodiversity, which impairs ecosystem functions and services. Therefore, understanding which processes shape how biodiversity is distributed along spatial and environmental gradients is a first step to guide conservation and management efforts. We aimed to determine the relative explanatory importance of biogeographic, environmental, landscape and spatial variables on assemblage dissimilarities and functional diversity of dung beetles along the Atlantic Forest–Pampa (i.e. forest–grassland) transition zone located in Southeast South America. We described each site according to their biogeographic position, environmental conditions, landscape features and spatial patterns. The compositional dissimilarity was partitioned into turnover and nestedness components of β‐diversity. Mantel tests and generalised dissimilarity models were used to relate β‐diversity and its components to biogeographic, environmental, landscape and spatial variables. Variation partitioning analysis was used to estimate the pure and shared variation in species composition and functional diversity explained by the four categories of predictors. Biome domain was the main factor causing dung beetle compositional dissimilarity, with a high species replacement between Atlantic Forest and Pampa. Biogeographic, environmental, landscape and spatial distances also affected the patterns of dung beetle dissimilarity and β‐diversity components. The shared effects of the four sets of predictors explained most of the variation in dung beetle composition. A similar response pattern was found for dung beetle functional diversity, which excluded biogeographic effects. Only the pure effects of environmental and spatial predictors were significant for species composition and functional diversity. Our results indicate that dung beetle species composition and functional diversity are jointly driven by environmental, landscape and spatial predictors with higher pure environmental and spatial effects. The forest–grassland transition zone promotes a strong species and trait replacement highly influenced both by environmental filtering and dispersal limitation.     

基于景观遗传学的滇金丝猴栖息地连接度分析

结合景观遗传学,应用最小费用距离模型对物种栖息地进行连接度分析,能够为生物多样性保护和自然保护区管理提供更加真实准确及可实践操作的指导。选取滇金丝猴这一珍稀濒危物种,结合景观遗传学,应用最小费用距离模型对其栖息地进行了连接度和潜在扩散廊道分析。并且通过连接度的分析和制图绘制出了更为准确的种群间潜在扩散廊道,确定了受人工障碍影响的廊道及敏感区域。结果表明,研究区内的5个亚群中,仅S3亚群内的5个猴群保持着较好的连接度,总体来说,各亚群内的连接度相对于各亚群间连接度保持的较好。除S3亚群中猴群间的潜在扩散廊道较为理想外,其余种群间的潜在扩散廊道均受人工斑块的影响,多数廊道被人工障碍阻断,或面临即将被阻断的情况,对于滇金丝猴的扩散交流影响较大。敏感区域多集中在中南部的3个亚群间,这些敏感区域应作为景观恢复及保护区规划的重要优先区域。     

Mycangia of the ambrosia beetle, Austroplatypus incompertus (Schedl) (Coleoptera: Curculionidae: Platypodinae)

Abstract  Ambrosia beetles have an obligate relationship with the ambrosia fungi that they feed on. This requires that the beetles have means to transport those fungi when they colonise new hosts. Some ambrosia beetles have special structures called mycangia to transport fungi in. This paper describes the mycangia of the ambrosia beetle Austroplatypus incompertus and illustrates how the mycangical hairs are probably used by the beetle to acquire fungal spores for transport. The mycangia and probable method of fungal acquisition of this species are compared with those of other ambrosia beetles.     

贺兰山甲虫物种丰富度分布格局及其环境解释

理解山地物种丰富度分布格局及其成因对于山地生物多样性保护具有重要意义。本文基于贺兰山地区甲虫31科252属469种的分布信息, 结合相关气候与生境异质性数据, 系统地探讨了贺兰山地区甲虫及6个优势科物种丰富度地理格局及其影响因素。结果表明, 甲虫物种丰富度及科属区系分化强度以贺兰山中段最高, 南段比北段高, 西坡比东坡高。基于183个栅格内物种分布的二元数据聚类分析, 贺兰山甲虫分布可分为北段强旱生景观甲虫地理群、中西段半湿生景观甲虫地理群、中东段及南段半旱生景观甲虫地理群3个地理群。冗余分析(RDA)表明年均温和年均降水量是影响最显著的因子。方差分解结果显示, 水分与能量因子共同解释了全部甲虫物种丰富度57.1%的空间变异, 单独解释率分别为5.9%和7.1%。生境异质性解释了全部甲虫物种丰富度35.2%的变异, 单独解释率仅为1.8%。气候因素与生境异质性对不同优势科物种丰富度的相对影响并不一致。在贺兰山的南段和北段, 生境异质性和水分因子对甲虫物种丰富度影响作用明显。水分和能量因子是贺兰山地区甲虫物种丰富度空间分布格局的主导因子, 生境异质性有助于提高甲虫物种丰富度。从未解释的比例来分析, 地形和土壤因素可能对贺兰山甲虫物种丰富度存在重要影响。     

Age and sex-dependent effects of landscape cover and trapping on the spatial genetic structure of the stone marten (<Emphasis Type="Italic">Martes foina</Emphasis>)

Maintenance of genetic variation is of critical importance for wild populations since low levels limit the species’ ability to respond to different threats (diseases, predators, environmental changes) in both the long and the short term. Human activities could impact the genetic variation of wild species in multiple ways, including via fragmentation and harvesting. We used an individual-based landscape genetics approach to describe the impact of landscape elements and trapping pressure on the spatial genetic structure of a large sample (n = 370) of the stone marten (Martes foina) in central-eastern France (Bresse). An analysis of isolation-by-resistance using a causal modeling approach showed an influence of landscape cover and/or trapping pressure on gene flow according to age and sex class. Overall, the connectivity in the study area is provided mainly by vegetation cover, while roads and open areas partially impede it. Unexpectedly for this “urban adapter” species, buildings could reduce gene flow. We also emphasized the sex-dependent effect of trapping on gene flow. Genetic differentiation in males was influenced by trapping pressure and landscape structure while only the latter influenced genetic differentiation in females. A stronger isolation by distance in males than in females suggested that at the scale of the study area, males are more exposed to trapping pressure, which reduces effective dispersal. Overall, the combination of both landscape and trapping costs might create an ‘ecological trap’ that could disrupt gene flow, leading to a north–south division in the study area.     

Expert-based versus habitat-suitability models to develop resistance surfaces in landscape genetics

Landscape genetics aims to investigate functional connectivity among wild populations by evaluating the impact of landscape features on gene flow. Genetic distances among populations or individuals are generally better explained by least-cost path (LCP) distances derived from resistance surfaces than by simple Euclidean distances. Resistance surfaces reflect the cost for an organism to move through particular landscape elements. However, determining the effects of landscape types on movements is challenging. Because of a general lack of empirical data on movements, resistance surfaces mostly rely on expert knowledge. Habitat-suitability models potentially provide a more objective method to estimate resistance surfaces than expert opinions, but they have rarely been applied in landscape genetics so far. We compared LCP distances based on expert knowledge with LCP distances derived from habitat-suitability models to evaluate their performance in landscape genetics. We related all LCP distances to genetic distances in linear mixed effect models on an empirical data set of wolves (Canis lupus) from Italy. All LCP distances showed highly significant (P ≤ 0.0001) standardized β coefficients and R ² values, but LCPs from habitat-suitability models generally showed higher values than those resulting from expert knowledge. Moreover, all LCP distances better explained genetic distances than Euclidean distances, irrespective of the approaches used. Considering our results, we encourage researchers in landscape genetics to use resistance surfaces based on habitat suitability which performed better than expert-based LCPs in explaining patterns of gene flow and functional connectivity.     

A meta‐analysis of isolation by distance: relic or reference standard for landscape genetics?

Isolation by distance (IBD) has been a common measure of genetic structure among populations and is based on Euclidean distances among populations. Whereas IBD does not incorporate geographic complexity (e.g. dispersal barriers, corridors) that may better predict genetic structure, a new approach (landscape genetics) joins landscape ecology with population genetics to better model genetic structure. Should IBD be set aside or should it persist as the most simple model in landscape genetics? We evaluated the status of IBD by collecting and analyzing results of 240 IBD data sets among diverse taxa and study systems. IBD typically represented a low proportion of variance in genetic structure (mean r²=0.22) in part because many studies included relatively few populations (mean=11). The number of populations studied (N) was asymptotically related to IBD significance; a study with 9 populations has only 50% probability of significance, while one with >23 populations will have 90% probability of significance. Surprisingly, ectothermic animals were significantly (p=0.0018) more likely to have significant IBD than endotherms, which suggests a metabolic basis underlying gene flow rates. We also observed marginally significant effects on IBD significance for a) taxa in general and b) dispersal modes within actively‐dispersing endotherms. Other factors analyzed (genetic markers, genetic distances, habitats, active or passive dispersal, plant growth form) did not significantly affect IBD, likely related to typical N. For multiple reasons we conclude that IBD should continue as the simplest reference standard against which all other, more complex models should be compared in landscape genetics research.     

Ecological metrics predict connectivity better than geographic distance

We use microsatellite loci to examine genetic structure of the Florida scrub lizard (Sceloporus woodi) and test for the effects of landscape variables at the scale of neighboring patches. We evaluate ecological metrics of connectivity with genetics data, which to our knowledge is the first application of these particular metrics to landscape-level genetics studies in Florida scrub. Florida scrub is a highly threatened ecosystem in which habitat patches are remnants of a previously widespread xeric landscape. Analysis of mitochondrial DNA (mtDNA) has shown that landscape structure influenced the evolutionary history of the Florida scrub lizard (S. woodi) across its range. Our results concur with these mtDNA studies in documenting divergence between xeric ridge systems and also demonstrate divergence at very local scales. Both least-cost distance and pairwise isolation (a metric used in ecological studies that includes patch size, quality and a modified isolation index) were better predictors of genetic distance than Euclidean distance, indicating that mesic and hydric habitat influence spatial patterns in genetic variation. Our results support the need for focusing on spatial distribution of scrub habitat at the scale of neighboring patches, as well as regionally, in conservation management and restoration. Also, our study points to the value of integrating landscape ecology metrics into landscape genetics.     

Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency in landscape genetic studies

Landscape genetics, an emerging field integrating landscape ecology and population genetics, has great potential to influence our understanding of habitat connectivity and distribution of organisms. Whereas typical population genetics studies summarize gene flow as pairwise measures between sampling localities, landscape characteristics that influence population genetic connectivity are often continuously distributed in space. Thus, there are currently gaps in both the ability to analyze genotypic data in a continuous spatial context and our knowledge of expected of landscape genetic structure under varying conditions. We present a framework for generating continuous “genetic surfaces”, evaluate their statistical properties, and quantify statistical behavior of landscape genetic structure in a simple landscape. We simulated microsatellite genotypes under varying parameters (time since vicariance, migration, effective population size) and used ancestry (q) values from STRUCTURE to interpolate a genetic surface. Using a spatially adjusted Pearson's correlation coefficient to test the significance of landscape variable(s) on genetic structure we were able to detect landscape genetic structure on a contemporary time scale (≥5 generations post vicariance, migration probability ≤0.10) even when population differentiation was minimal (F_ST≥0.00015). We show that genetic variation can be significantly correlated with geographic distance even when genetic structure is due to landscape variable(s), demonstrating the importance of testing landscape influence on genetic structure. Finally, we apply genetic surfacing to analyze an empirical dataset of black bears from northern Idaho USA. We find black bear genetic variation is a function of distance (autocorrelation) and habitat patch (spatial dependency), consistent with previous results indicating genetic variation was influenced by landscape by resistance. These results suggest genetic surfaces can be used to test competing hypotheses of the influence of landscape characteristics on genetic structure without delineation of categorical groups.