The blacklegged tick, Ixodes scapularis, is a vector of Borrelia burgdorferi sensu stricto (s.s.), the causative agent of Lyme disease, part of a slow-moving epidemic of Lyme borreliosis spreading across the northern hemisphere. There are well-known geographic differences in the vectorial capacity of these ticks associated with genetic variation. Despite the need for detailed genetic information in this disease system, previous phylogeographic studies of these ticks have been restricted to relatively few populations or genetic loci. Here we present the most comprehensive phylogeographic study of I. scapularis conducted by using 3RAD and surveying 353 ticks from 33 counties throughout the range of I. scapularis. We found limited genetic variation among populations from the Northeast and Upper Midwest, where Lyme disease is most common, and higher genetic variation among populations from the South. We identify four genetic clusters of I. scapularis that are consistent with four major geographic regions, plus a distinct Central Florida group. In regions where Lyme disease is increasing in frequency, the I. scapularis populations genetically group with ticks from historically highly Lyme-endemic regions. Finally, we identify ten variable DNA sites that contribute the most to population differentiation. These variable sites cluster on one of the chromosome-scale scaffolds for I. scapularis and are within identified genes. Our findings illuminate the need for additional research to identify loci causing variation in the vectorial capacity of I. scapularis and where additional tick sampling would be most valuable to further understand disease trends caused by pathogens transmitted by I. scapularis.
Accumulating evidence for trade-offs involving metabolic traits has demonstrated their importance in evolution of organisms. Metabolic models with different level of complexity have already been considered when investigating mechanisms that explain various metabolic trade-offs. Here we provide a systematic review of modelling approaches that have been used to study and explain trade-offs between: (i) kinetic properties of individual enzymes, (ii) rates of metabolic reactions, (iii) rate and yield of metabolic pathways and networks, (iv) different metabolic objectives in single organisms and in metabolic communities, and (v) metabolic concentrations. In providing insights into mechanisms underlying these five types of metabolic trade-offs obtained from constraint-based metabolic modelling, we emphasize the relation of metabolic trade-offs to the classical black box Y-model that provides conceptual explanation for resource acquisition-allocation trade-offs. In addition, we identify several pressing concerns and offer a perspective for future research in the identification and manipulation of metabolic trade-offs by relying on the toolbox provided by constraint-based metabolic modelling for single organisms and microbial communities.
The wide geographical distribution of Eurasian wild boar (Sus scrofa) provides a natural model to study the adaptation to cold climate. Here, we conducted whole-genome sequencing and analyses for wild boar populations from cold (northern and northeastern Asia) and relatively warm regions (southeastern Asia and southern China). With genome-wide scans of four methods, we detected candidate genes underlying cold-adaptation with significant enrichment of pathways related to thermogenesis, fat cell development, and adipose tissue regulation. We further found two positively selected variants, rs341219502 in IGF1R (Insulin-Like Growth Factor 1 Receptor) and rs327139795 in BRD4 (Bromodomain Containing 4), which showed the highest cold-warm differentiation among all regulatory and exonic variants, respectively. Allele frequency distribution revealed that they are absent in outgroup species and warm-region wild boar but nearly fixed in cold-region populations, suggesting their de novo origins in cold-region populations. The historical demography during the last 25,000-50,000 years does not support the hypothesis that the sweep signal on the two variants resulted from genetic drift. We also found three genes (SLCO1C1, PDE3A, and TTC28) with selection signals in both wild boar and indigenous human populations from Siberia, which suggests convergent molecular adaptation in mammals. Our study indicates that molecular adaptive evolution is underlying the remarkable environmental flexibility of wild boar.
With continued global change, recovery of species listed under the Endangered Species Act is increasingly challenging. One rare success was the recovery and delisting of the Channel Island fox (Urocyon littoralis) after 90-99% population declines in the 1990s. While their demographic recovery was dramatic, less is known about their genetic recovery. To address genetic changes we conducted the first multi-individual and population-level direct genetic comparison of samples collected before and after the recent bottlenecks. Using whole exome sequencing, we found that already genetically depauperate populations were further degraded by the 1990s declines and remain low, particularly on San Miguel Island which underwent one of the most severe bottlenecks. The three other islands that experienced recent bottlenecks (Santa Rosa, Santa Cruz, and Santa Catalina islands) showed mixed results based on multiple metrics of genetic diversity. Previous island fox genomics studies showed low genetic diversity before the declines and no change after the demographic recovery, thus this is the first study to show a decrease in genetic diversity over time in U. littoralis. Additionally, we found that divergence between populations consistently increased over time, complicating prospects for using inter-island translocation as a conservation tool. The Santa Catalina subspecies is now federally listed as threatened, yet other de-listed subspecies are still recovering genetic variation which may limit their ability to adapt to changing environmental conditions. This study further demonstrates that species conservation is more complex than population size and that some island fox populations are not yet “out of the woods”.
According to prevailing theory, sexually reproducing animals adapt to different environments by the production of phenotypic variation from the standing genetic variation and selection of the most suited phenotypes. Contrary to all expectations, asexually reproducing animals can also inhabit broad ranges of geographical latitudes, altitudes and habitats, despite virtual genetic identity. Recent whole genome analyses of differently adapted clonal populations and genetically impoverished invaders revealed that they can use epigenetic variation instead of genetic variation to stably adapt to different environments. The required phenotypes are produced from the same DNA sequence via changes in gene expression, which is trigged by strong environmental cues and mediated by environment-sensitive epigenetic mechanisms like DNA methylation. Habitat-specific epigenetic fingerprints were maintained over subsequent years, pointing at the existence of epigenetic ecotypes. Obviously, all animals can produce different phenotypes from the same DNA sequence, but in asexually reproducing populations, genetically impoverished invaders, sessile taxa and species with long generation times it is apparently of prime importance. In contrast to beneficial genetic mutations and meiotic gene combinations that require many generations to be established in a population, environmentally-induced epigenetic changes and subsequent alterations in gene and phenotype expression affect population members synchronously in the first exposed generation, providing an ideal means for fast, directional adaptation to changing conditions. The production of different phenotypes from the same genome in response to different environmental cues via epigenetic mechanisms is also suitable to explain the “general-purpose genotype” and the “genetic paradox of invasion”.
Increasing evidence suggests that fungal communities are key components of biogeochemical cycles in coastal ecosystems. While several studies highlighted strong spatial patterns in fungal abundance and diversity, there are very few studies using a more integrative approach to study the spatio-temporal distribution of fungi, taking also the active part of the community into account. To better understand the consequences of anthropogenic activities, e.g. marine aquaculture, for fungal community composition and activities, we simultaneously evaluated the temporal (four different seasons) and spatial dynamics in total (DNA) and active (RNA) fungal communities in relation to several major physicochemical properties. Fungal communities were highly diverse, but showed the ubiquitous dominance of Dikarya and the occasional predominance of Glomeromycota, Mucoromycota, Mortierellomycota, Chytridiomycota, Mortierellomycota, Olpidiomycota, and Rozellomycota. Thereby, fungal diversity indices showed a much higher seasonal variation than with the degree of aquaculture activity, for both total and active communities. This notion is supported by co-occurrence networks exhibiting a clear seasonal pattern. Furthermore, fungal community structure in coastal waters showed distinct relationships with environmental factors varying both with season and in space. For both, total and active fungal communities, a combination of environmental variables such as temperature, DO and NO2- exhibited the greatest impact on community structure. Our study demonstrates a distinct spatio-temporal dynamics of both, total and active fungi and provides a foundation to better understand the ecological roles of marine fungi in coastal ecosystems in relation to mariculture activities.
The purplish bifurcate mussel Mytilisepta virgata is widely distributed and represents one of the major components of the intertidal community in the northwestern Pacific (NWP). Here, we characterized population genetic structure of NWP populations throughout their whole distribution range using both mitochondrial (mtDNA cox1) and nuclear (ITS1) markers. Population genetic analyses for mtDNA cox 1 sequences revealed two monophyletic lineages (i.e., southern and northern lineages) geographically distributed according to the two different surface water temperature zones in the NWP. The timing of the lineage split is estimated at the Pliocene- mid-Pleistocene (5.49-1.61 Mya), which is consistent with the timing of the historical isolation of the East Sea/Sea of Japan from the South and East China Seas caused by sea level decline during glacial cycles. Historical sea level fluctuation during the Pliocene-Pleistocene and subsequent adaptation of mussels to different surface water temperature zones may have contributed to shaping the contemporary genetic diversity and deep divergence of the two mitochondrial lineages. Unlike mtDNA sequences, a clear lineage splitting between the two mitochondrial lineages was not found in ITS1 sequences, showing a star-like structure that is composed of a mixture of southern and northern mitochondrial lineages. Possible scenarios are proposed to explain this type of mito-nuclear discordance: stochastic divergence in the coalescent processes of the two molecular markers, or balancing selection under different marine environments. Future work is required to address whether the thermal physiology of these mussels correlates with the deep divergence of their mitochondrial genes.
Despite the success of the United States (US) Boll Weevil Eradication Program, the boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), remains a threat to cotton production in the southern US and is arguably the most important cotton pest in Central and South America. Management of this species is complicated by the existence of morphologically similar variants and re-infestations of areas where eradication had been successful. To date, no study has applied a high-throughput sequencing approach to better understand the population genetic structure of the boll weevil. Furthermore, only a single study has investigated genetic relationships between populations in North and South America. Here, we used double digest restriction site-associated DNA sequencing (ddRADseq) to resolve the population genomic structure of the boll weevil in the southern US, northern Mexico, and Argentina, test the two-form and three-form hypotheses of boll weevil variation in North America using a phylogeographic approach, and determine the relationship of the South American populations to the North. Our results supported the two-form hypothesis of boll weevil variation in North America wherein there are two major genetic lineages – one consisting of populations found geographically west of the Sierra Madre Occidental mountain range and the second consisting of populations found to the east – both are highly sub-structured across space and time. Boll weevil populations from Argentina were more closely related to the eastern lineage, suggesting a range expansion by the eastern lineage, but additional sampling across Central and South America is needed to determine a probable origin.
The rapid stem elongation of the invasive weed Mikania micrantha in the forest understory is of vital significance for its successful invasion. To understand the physiological and molecular mechanisms for this process, here we comparatively investigated the physiological characteristics and transcriptome patterns of M. micrantha stem under low light (30%) and full light (100%) conditions. The results showed that M. micrantha stem had photosynthetic capacity, which was highly plastic to light intensities, constituting of an indispensable part of the plastic response of M. micrantha to shading. M. micrantha had longer internodes, epidermal cells, and consequently longer stems under low light than full light conditions, which could be attributed to the reduced photoprotective substances (flavonoid and anthocyanin) and increased synthesis of phytohormones (gibberellin, GA and Auxin) as observed under shading treatment. The transcriptome sequencing and qPCR verified the results from physiological investigation, and showed that under low light condition the expression levels of genes involving in photosynthesis (e.g. MmPsaA, MmPsbO1 and MmFd3) were generally down-regulated in comparison to full light condition, so were the genes related to the photoprotective substances synthesis (e.g. MmCHS, and MmF3H1) and the negative regulators of phytohormone (e.g. MmAUX1, MmRR1 and MmGAI). It was concluded that the regulation of phytohormones and photoprotective substances are the important material basis for the rapid elongation of M. micrantha stems with high plasticity, which really matters to the vine to have high invasiveness in the forest understory.
The star barnacle, Chthamalus stellatus Poli, populates the Mediterranean Sea, the North-Eastern Atlantic coasts, and the offshore Eastern Atlantic islands. Previous studies have found apparent genetic differences between the Atlantic and the Mediterranean populations of C. stellatus, suggesting possible geological and oceanographic explanations for these differences. We have studied the genetic diversity of 14 populations spanning from the Eastern Atlantic to the Eastern Mediterranean, using 63 genomic polymorphic sites. We have found that these populations form four distinct clusters: Eastern Atlantic, Western Mediterranean, Mid-Mediterranean and Eastern Mediterranean, with evident connectivity between them. We examined here environmental conditions like surface currents, water salinity and temperature as probable factors that have formed the population structure. We suggest that C. stellatus is a suitable marine animal for studying how geological events and hydrographic conditions shape the fauna in the Mediterranean Sea.
Trichoderma is a fungal genus comprising species used as biocontrol agents in crop plant protection and with high value for industry. The beneficial effects of these species are supported by the secondary metabolites they produced. Terpenoid compounds are key players in the interaction of Trichoderma spp. with the environment and with their fungal and plant hosts, however most of the terpene synthase (TS) genes involved in their biosynthesis have yet not been characterized. Here, we combined comparative genomics of TSs of 21 strains belonging to 17 Trichoderma spp., and gene expression studies on TSs using T. gamsii T6085 as a model. An overview of the diversity within the TS-gene family and the regulation of TS genes is provided. We identified 15 groups of TSs, and the presence of clade-specific enzymes revealed a variety of terpenoid chemotypes evolved to cover different ecological demands. We propose that functional differentiation of gene family members is the driver for the high number of TS genes found in the genomes of Trichoderma. Expression studies provide a picture in which different TS genes are regulated in many ways, a strong indication of different biological functions.
Antheraea proylei J, is an economically important silkworm of North Eastern region of India reared for the production of the tasar silk. The silkworm is often exposed to various microbial diseases caused by bacteria and viruses. The disease causes significant damage to larvae and elicit pupal mortality, thus posing a serious threat to the linked economic activities. The gut microbiome of silkworms play an important role, in nutrient acquisition and immunity. In this study, we have reported molecular characterization and histopathological assessment of gut associated bacteria of healthy and diseased tasar silkworms. As compared to healthy silkworms, diseased infected silk glands shows loss of turbidity, secretory layer not distinguishable to tunica propria and lumen distorted. Both secretory and absorptive cells were found to be hypertrophied. Body fat becomes vacuolated and soft when compared to the healthy silkworms. Bacterial profile of healthy and diseased silkworm respectively was identified by 16S rRNA gene sequencing and analysis. Bacillus toyonensis and Bacillus thuringiensis were commonly found in healthy larvae whereas Bacillus aryabhattai and Bacillus megaterium were found in diseased larvae. The family Bacillus of phylum Firmicutes was dominant in both healthy and diseased silkworms. To the best of our knowledge, this is the first attempt to study A. proylei midgut microbiota from a biodiversity hotspot in North Eastern India. The present study might be helpful in disease prognosis and further comprehensive analysis on midgut microflora may lead towards the development of effective strategies for management of these economic silkworms.
Pine wilt disease (PWD), Bursaphelenchus xylophilus, is an extremely threatening invasion forest disease throughout the world, especially in Asia. B. xylophilus is spread in Asia by vector beetles of Monochamus alternatus, which has long no effective control method. Understanding of landscape effects on the dispersal and outbreaks of forest pests is crucial to establishing effective ecological control strategies. Here, we analyzed the samples of M. alternatus collected at landscapes in order to estimate the effects of landscape types on the genetic structure and dispersal of M. alternatus. The landscapes included the geographical scales, forest types and land uses. The individuals of M. alternatus were genotyped by using whole-genome resequencing. Population genetic structures were clearly differentiated at the intermediate scale, suggesting the intermediate scale is an effective barrier against natural dispersal of M. alternatus. We used the least-coat distances, least-cost transect analysis, and distance-based redundancy analysis to estimate the effects of forest types and land uses within the fine scales. The results showed that the gene flow and genetic diversity were positively correlated with host and mixed forests, whereas negatively with non-host forests. Among land-use landscapes, the roads had the positive effect on gene flow and genetic diversity but farmland and urban uses had negative effects. This highlights that human-mediated transport via roads was likely to be the main factor leading to the long-distance invasion of M. alternatus, whereas non-host landscapes could suppress the spread of this species. These findings may be useful to control the PWD dispersed by M. alternatus.
Rickettsia are intracellular bacteria best known as the causative agents of human and animal diseases. Although these medically important Rickettsia are often transmitted via haematophagous arthropods, other Rickettsia, such as those in the Torix group, appear to reside exclusively in invertebrates and protists with no secondary vertebrate host. Importantly, little is known about the diversity or host range of Torix group Rickettsia. This study describes the serendipitous discovery of Rickettsia amplicons in the Barcode of Life Data System (BOLD), a sequence database specifically designed for the curation of mtDNA barcodes. Out of 184,585 barcode sequences analysed, Rickettsia is observed in approximately 0.41% of barcode submissions and is more likely to be found than Wolbachia (0.17%). The Torix group of Rickettsia are shown to account for 95% of all unintended amplifications from the genus, with a multilocus analysis of these strains revealing this symbiont commonly shifts between distantly related host taxa. A further targeted PCR screen of 1,612 individuals from 169 terrestrial and aquatic arthropod species identified mostly Torix strains (14/16) and supports the “aquatic hotspot” hypothesis for Torix infection. Furthermore, the analysis of Sequence Read Archive (SRA) deposits indicates Torix infections represent a significant proportion of all Rickettsia symbioses. This combination of methods reveals a broad host diversity associated with Torix Rickettsia including phloem-feeding bugs, parasitoid wasps, forest detritivores and vectors of disease. The unknown host effects and transmission strategies of these endosymbionts makes these newly discovered associations important to inform future directions of investigation involving the understudied Torix Rickettsia.
Four bacterial strains were isolated from enrichment cultures inoculated with soil from Bien Hoa military base in Vietnam contaminated with the herbicides 2,4-dichlorophenoxyacetate (2,4-D) and 2,4,5-trichlorophenoxyacetate (2,4,5-T). They were classified as Pseudomonas aeruginosa BT1 2.2, Sphingomonas histidinilytica BT1 5.2, Bordetella petrii BT1 9.2, and Achromobacter xylosoxidans BT1 10.2, respectively. All 4 of them were able to degrade 2,4-D and 2,4,5-T during cultivation, but only the last 3 species used them as sole sources of carbon and free energy. We obtained a comprehensive insight into their degradation pathways by genomic analysis of these strains. A gene cluster with tfdCDEF genes was found in A. xylosoxidans BT1 10.2. The gene organization along with the amino acid sequences of the gene products are almost identical to those in B. petrii DSM12804. The B. petrii BT1 9.2 strain that we isolated has a full complement of the tfdABCDEF genes. Surprisingly, the gene organization along with the amino acid sequences of the gene products are virtually identical to those of Cupriavidus pinatubonensis JMP134, referred to as type I tfd genes, and clearly different from those of A. xylosoxidans and B. petrii DSM12804. Altogether, our enrichment approach has successfully resulted in boosting 3 different types of proteobacterial species that are equipped with metabolic pathways to use the herbicides as sole sources of carbon and free energy. We hypothesize that some of the corresponding genetic potential may have been recruited in recent mating events between these species and other members of the β- and γ-proteobacteria.
The relationship of host and symbionts is complex and dynamic. Symbionts can significantly impact host phenotypes and parasite epidemics may be influenced by interactions among symbionts. Aphids are well known for their symbiotic associations with bacteria. However, few studies have examined the offsprings of parasitized host and the ecological implications of a dynamic microbiome longitudinaly. In the present study, we surveyed the microbiota in non-parasitized aphids and parasitized aphids its offspring for over four consecutive generations by using high-throughput 16S rRNA sequencing. Across hosts, parasite strongly altered symbiont composition of parasitized aphids offspring, especially in the fourth generation. Moreover, parasitism reduced weight and reproductive capacity of the parasitized offspring and influenced parasite epidemics. Taken together, these results indicate that parasitoids can influence host-microbiome interactions by altering the symbionts composition in the host offspring. Our findings further supports the importance host-parasite-microbiome tirad interactions, which can create intense reciprocal selection resulting in coevolution between species.
Hybridization has fascinated biologists in recent centuries for its evolutionary importance, especially in plants. Hybrid zones are commonly located in regions across environmental gradients due to more opportunities to contact and ecological heterogeneity. For aquatic taxa, intrazonal character makes broad overlapping regions in intermediate environments between related species. However, we have limited information on the hybridization pattern of aquatic taxa across an altitudinal gradient. In this study, we aimed to test the hypotheses that niche overlap and hybridization might be extensive in related aquatic plants in alpines. We evaluated the niche overlap in three related species pairs on the Qinghai-Tibetan Plateau and assessed the spatial pattern of hybrid populations. Obvious niche overlap and common hybridization were revealed in all three pairs of related aquatic plants. The plateau edge and river basins were broad areas for the sympatry of divergent taxa, where a large proportion of hybrid populations occurred. Hybrids are also discretely distributed in diverse habitats on the plateau. Differences in the extent of niche overlap, genetic incompatibility and phylogeographic history might lead to inconsistences in hybridization patterns among the three species pairs. Our results suggested that plateau areas are a hotspot for ecologically divergent aquatic species to contact and mate and implied that hybridization may be important for the freshwater biodiversity of highlands.
Facultative, heritable endosymbionts are found at intermediate prevalence within most insect species, playing frequent roles in their hosts’ defense against environmental pressures. Focusing on Hamiltonella defensa, a common bacterial endosymbiont of aphids, we tested the hypothesis that such pressures impose seasonal balancing selection, shaping a widespread infection polymorphism. In our studied pea aphid (Acyrthosiphon pisum) population, Hamiltonella infection frequencies ranged from 23.2% to 68.1% across a six-month longitudinal survey. Rapid spikes and declines were consistent across fields, and we estimated that selection coefficients, for Hamiltonella-infected aphids, changed sign within this single season. Prior laboratory research suggested anti-parasitoid defense as the major Hamiltonella benefit, and costs under parasitoid absence. While a prior field study supported these forces as counter-weights in a regime of seasonal balancing selection, our present survey showed no significant relationship between parasitoid wasps and Hamiltonella. Field cage experiments provided some explanation: parasitoids drove ~10% boosts to Hamiltonella frequencies that would be hard to detect under less controlled conditions. They also showed that Hamiltonella was not always costly under parasitoid exclusion, contradicting another long-held prediction. Instead, our longitudinal survey – and two overwintering studies - showed temperature to be the strongest predictor of Hamiltonella infection, matching some lab discoveries, and suggesting thermally sensitive costs and benefits, unrelated to parasitism, can shape this symbiont’s prevalence. These results add to a growing body of evidence arguing for rapid, seasonal adaptation in multivoltine organisms. For many insects, such adaptation may be mediated through the diverse impacts of heritable symbionts on host phenotypes.