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.

Environmental temperature serves a major driver for adaptive changes in wild organisms, however, its role in domestication has been less characterized. To uncover the mechanisms of cold tolerance in domestic animals, we sequenced genomes of 28 cattle at median coverage from warm and cold areas across China. By characterizing the population structure and demographic history, we identified two genetic clusters, i.e., northern and southern cattle groups, and a common historic population peak at 30 kilo years ago. Genome scan of cold tolerant breeds revealed genes that under selection sweeps enriched in thermogenesis related pathways. Specifically, we determined a substitution of PRDM16 (p.P779L) in north cattle, which maintains the formation of brown adipocytes through boosting expression of thermogenic related genes, indicating a vital role of this gene in cold tolerance. The findings provide a basis of genetic variations in domestic cattle that shaped by temperature environments and highlight a role of reverse mutation in livestock species.

Organisms exposed to endocrine disruptors in early life can show altered phenotype later in adulthood. Although the mechanisms underlying these long-term effects remain poorly understood, an increasing body of evidence points toward the potential role of epigenetic processes. In the present study, we exposed hatchlings of an isogenic lineage of the self-fertilizing fish mangrove rivulus for 28 days to 4 and 120 ng/L of 17-α-ethinylestradiol. After a recovery period of 140 days, reduced representation bisulfite sequencing (RRBS) was performed on the liver in order to assess the hepatic genome-wide methylation landscape. Across all treatment comparisons, a total of 146 differentially methylated fragments (DMFs) were reported, mostly for the group exposed to 4 ng/L, suggesting a non-monotonic effect of EE2 exposure. Gene ontology analysis revealed networks involved in lipid metabolism, cellular processes, connective tissue function, molecular transport and inflammation. The highest effect was reported for nipped-B-like protein B (NIPBL) promoter region after exposure to 4 ng/L EE2 (+ 21.9%), suggesting that NIPBL could be an important regulator for long-term effects of EE2. Our results also suggest a significant role of DNA methylation in intergenic regions and potentially in transposable elements. These results support the ability of early exposure to endocrine disruptors of inducing epigenetic alterations during adulthood, providing plausible mechanistic explanations for long-term phenotypic alteration. Additionally, this work demonstrates the usefulness of isogenic lineages of the self-fertilizing mangrove rivulus to better understand the biological significance of long-term alterations of DNA methylation by diminishing the confounding factor of genetic variability.

Biomonitoring of complex heterogeneous environments is highly challenging. Fish in deep water bodies occupy different habitats, therefore a combination of survey methods has traditionally been used. Environmental DNA (eDNA) metabarcoding is a novel monitoring tool that can overcome spatial heterogeneity in a highly sensitive and entirely non-invasive manner. However, taxon detection probability is dependent on real-time environmental variables. In this study, three reservoirs were sampled in two seasons using a spatiotemporally distributed sampling design covering major environmental gradients. In all sampling campaigns, 31 fish taxa were detected which exceeded expectations. Data reliability was confirmed by a tight positive correlation between individual taxon scores derived from gillnet sampling and eDNA site occupancy. Analyses confirmed anticipated trends, such as the highest number of taxa were observed in the largest water body, and more taxa were detected in inflows and littoral regions compared to open water. The most important factors for fish distribution were temperature, age and trophic status (expressed as total Chlorophyll a concentration) of water bodies. Taxon detection reflected ecological niches of individual species, e.g. warm water wels catfish (Silurus glanis) and cold water salmonids. This study provides further evidence that eDNA metabarcoding is suitable for ecological study in heterogeneous environments and may substitute conventional fish sampling techniques.

Both aquatic and terrestrial biodiversity information can be detected in riverine water environmental DNA (eDNA). However, the monitoring effectiveness (i.e., the proportion of aquatic and terrestrial biodiversity information detected in riverine water eDNA samples) is unknown. To investigate the monitoring effectiveness, we introduced the concept of watershed biological information flow (WBIF) and proposed that the monitoring effectiveness depended on the transportation effectiveness of the WBIF. Then, the monitoring effectiveness could be assessed in the WBIF framework. Here, we conducted a monitoring effectiveness assessment case study in a watershed on the Qinghai-Tibet Plateau according to analysis of the bacterial operational taxonomic unit (OTU) assemblages detected in riverine water eDNA samples and riparian soil eDNA samples during three seasons. The results showed that (1) the downstream-to-upstream monitoring effectiveness: only 76% of the bacterial OTUs could be detected 1 km downstream in spring and more than 97% and 96% could be detected in summer and autumn, respectively. (2) The river-to-land monitoring effectiveness: more than 62% of the bacterial OTUs in riparian soil eDNA samples could be detected in adjacent riverine water eDNA samples on rainy summer days and 16% and 48% could be detected on cloudy spring and autumn days, respectively. These results suggested that riverine water eDNA was viable for simultaneously monitoring aquatic and terrestrial bacterial biodiversity and that rainy days in summer or autumn were suitable sampling times on the Qinghai-Tibet Plateau. More studies on monitoring effectiveness in other taxonomies and in other watersheds with different climatic conditions are needed.

The mountains of southern China are an excellent system for investigating the processes driving the geographic distribution of biodiversity and radiation of plant populations in response to Pleistocene climate fluctuations. How the key mountain ranges in southern China have affected the evolution of narrowly distributed species is less studied than more widespread species. Here we focused on Cercis chuniana, a woody species endemic to the southern mountain ranges in subtropical China, to elucidate its population dynamics. We used genotyping by sequencing (GBS) to investigate the spatial pattern of genetic variation among 11 populations. Bayesian time estimation revealed that population divergence occurred in the middle Pleistocene, when populations in the Nanling Mts. separated from those to the east. Geographical isolation was detected between the populations located in adjacent mountain ranges, thought to function as geographical barriers due to their complex physiography. As inferred by ecological niche modeling and coalescent simulations, secondary contact occurred during the warm Lushan-Tali interglacial period in China, with intensified East Asia summer monsoon and continuous habitat available for occupation. Complex physiography plus long-term stable ecological conditions across glacial cycles facilitated the demographic expansion in the Nanling Mts., from which contemporary migration began. Our work shows that population genomic approaches are effective in detecting the population dynamics of narrowly distributed species. This study advances our understanding how glacial cycles have affected the evolutionary history of plant species in southern China montane ecosystems.

Intestine regeneration in the sea cucumber Apostichopus japonicus is a fascinating biological event and a typical example for studying host-intestinal microbiota interactions. The intestinal microbiota may play important roles in developing intestine promotion, but the underlying mechanism remains unclear. Notably, altered microbiota abundance may be a key marker of the observed ecosystem. To understand the role of the developing intestinal microbiota in intestine regeneration via quantitative data, we developed a germ-free sea cucumber model and analyzed the intestinal microbial differentiation of faster and slower regenerating A. japonicus individuals during intestine regeneration. The results revealed that depletion of the intestinal microbiota resulted in elevated abundance of the potential key players Flavobacteriaceae and Rhodobacterales during intestine regeneration and thus promoted the intestine regeneration rate of A. japonicus. These results first revealed a direct link between intestinal microbial quantity and microbiome features and the intestinal regrowth rate of A. japonicus. Metagenomic analysis revealed that the increased abundance of Flavobacteriaceae elevated the enrichment of genes associated with carbohydrate utilization, whereas the abundant Rhodobacteraceae -enriched genes were associated with polyhydroxybutyrate production. We identified microbiota abundance as a key driver of microbial community alterations, especially beneficial microbiota members, in the developing intestine of A. japonicus. This study provides new insights into the mechanism of host-microbiota interactions related to intestine development, and the understanding of molecular diversity to questions within intestinal ecology.

Invasive species are of increasing concern to the local biodiversity and ecology as the magnitude of biological invasions is increasing globally. The genetic structures of newly established invasive populations may reveal insights towards the invasion processes, making population genetics an important tool for understanding current invasions. Here we study newly established populations (<10-20 years before first sampling) of the cosmopolitan alien ascidian Botryllus schlosseri in four Puget Sound (Washington, USA) marinas, using eight polymorphic microsatellites. Up to seven sampling sessions over a period of 19 years revealed populations with fluctuating allelic richness (AR=2.693-4.417) and gene diversity (He=0.362-0.589). The populations were well differentiated on spatial and temporal scales and subjected to moderate genetic drift (Fs’=0.027-0.071). The obtained significant heterozygote deficiencies, positive inbreeding coefficients (Fis) and population structure measures (Fst) revealed that no population was under the Hardy-Weinberg equilibrium. Comparing these parameters with those from two Californian sites (Moss Landing and Santa Cruz, 1200 km southerly; invaded by Botryllus during 1940’s) revealed a connection between Moss Landing and Puget Sound, while Santa Cruz remained isolated. On the US west coast scale, this study revealed no major difference in invasive population dynamics between recently and decade long established populations, except for fewer alleles and lower He. When comparing ten worldwide sites, only few microsatellite loci displayed strong regional differences. With globally the lowest numbers of alleles and lowest genetic indices, the Puget Sound Botryllus populations exhibit genetic characteristics of recently established populations, further emerging as one of the youngest B. schlosseri populations, worldwide.

Suitable habitat fragment size, isolation, and distance from a source are important variables influencing community composition of plants and animals, but the role of these environmental factors in determining composition and variation of host-associated microbial communities is poorly known. In parasite-associated microbial communities, it is hypothesized that evolution and ecology of an arthropod parasite will influence its microbiome more than broader environmental factors, but this hypothesis has not been extensively tested. To examine the influence of the broader environment on the parasite microbiome, we applied high-throughput sequencing of the V4 region of 16S rRNA to characterize the microbiome of 222 obligate ectoparasitic bat flies (Streblidae and Nycteribiidae) collected from 155 bats (representing six species) from ten habitat fragments in the Atlantic Forest of Brazil. Parasite species identity is the strongest driver of microbiome composition. To a lesser extent, reduction in habitat fragment area, but not isolation, is associated with an increase in connectance and betweenness centrality of bacterial association networks driven by changes in the diversity of the parasite community. Controlling for the parasite community, bacterial network topology covaries with habitat patch area and exhibits parasite-species specific responses to environmental change. Taken together, habitat loss may have cascading consequences for communities of interacting macro- and microorgansims.  

The whitefly Bemisia tabaci is a closely related group of > 35 cryptic species that feed on the phloem sap of a broad range of host plants. Species in the complex differ in their host-range breadth, but the mechanisms involved remain poorly understood. We investigated, therefore, how six different B. tabaci species cope with the environmental unpredictability presented by a set of four common and novel host plants. Behavioural studies indicated large differences in performances on the four hosts and putative specialization of one of the species to cassava plants. Transcriptomic analyses revealed two main insights. First, a large set of genes involved in metabolism (> 85%) showed differences in expression between the six species, and each species could be characterized by its own unique expression pattern of metabolic genes. However, within species, these genes were constitutively expressed, with a low level of environmental responsiveness (i.e., to host change). Second, within each species, sets of genes mainly associated with the super-pathways “environmental information processing” and “organismal systems”, responded to the host switching events. These included genes encoding for proteins involved in sugar homeostasis, signal transduction, membrane transport and immune, endocrine, sensory and digestive responses. Our findings suggested that the six B. tabaci species can be divided into four performance/transcriptomic “Types” and that polyphagy can be achieved in multiple ways. However, polyphagy level is determined by the specific identity of the metabolic genes/pathways that are enriched and overexpressed in each species (the species’ individual metabolic “tool kit”).

Flying fox (Pteropus hypomelanus) belongs to the frugivorous bats, which play a crucial role in maintaining proper functioning of an ecosystem and conservation of environment. Bats are well known carriers of pathogenic viruses such as BatCov RaTG13 from the coronavirus family that share 90.55% with SARS-CoV-2, the pathogen causing recent global pandemic coronavirus disease 19 (COVID-19). However, bats’ possible role as a carrier of pathogenic bacteria is less explored. Here, using metagenomic analysis through high-throughput sequencing, we explored the gut microbiome composition of different island populations on the east and west coasts of Peninsula Malaysia. The 16S rRNA gene in samples from Redang Island, Langkawi Island, Pangkor Island and Tinggi Island was amplified. Bacterial community composition and structure were analyzed with α and β diversity metrics. In contrast to recent studies of host-microbe associations in other mammals, we found no correlation between host phylogeny and bacterial community dissimilarity across four island populations. Our analyses suggest that the significant linear relationship between Redang Island and Langkawi Island implies high bacteria diversity which supporting latitudinal correlation. We found geographic locality is a strong predictor of microbial community composition and observed a positive correlation between ecological features and bacterial richness.

Whilst climate change is recognised as a major future threat to biodiversity, most species are currently threatened by extensive human-induced habitat loss, fragmentation and degradation. Tropical high altitude alpine and montane forest ecosystems and their biodiversity are particularly sensitive to temperature increases under climate change, but they are also subject to accelerated pressures from land conversion and degradation due to a growing human population. We studied the combined effects of anthropogenic land-use change, past and future climate changes and mountain range isolation on the endemic Ethiopian Highlands long-eared bat, Plecotus balensis, an understudied bat that is restricted to the remnant natural high altitude Afroalpine and Afromontane habitats. We integrated ecological niche modelling, landscape genetics and model-based inference to assess the genetic, geographic and demographic impacts of past and recent environmental changes. We show that mountain range isolation and historic climates shaped population structure and patterns of genetic variation, but recent anthropogenic land-use change and habitat degradation are associated with a severe population decline and loss of genetic diversity. Models predict that the suitable niche of this bat has been progressively shrinking since the last glaciation period. This study highlights threats to Afroalpine and  Afromontane biodiversity, squeezed to higher altitudes under climate change while losing genetic diversity and suffering population declines due to anthropogenic land-use change. We conclude that the conservation of tropical montane biodiversity requires a holistic approach, using genetic, ecological and geographic information to understand the effects of environmental changes across temporal scales and simultaneously addressing the impacts of multiple threats.

Population and conservation genetics seek to understand how adaptive diversity is shaped by the interweaving forces of molecular evolution in small and endangered populations. On the one hand, selection shapes variation, on the other hand, genetic drift impedes the selection by stochastic changes of allele frequencies. Drift is hypothesised to prevail if the population size is small. However, in practice empirical estimates of the population size are often challenging. Here we used island size as a proxy to population size to reveal the evolutionary constraints of molecular diversity in Toll-like receptors (TLRs) of mockingbirds (genus Mimus) inhabiting Galápagos islands. TLRs are crucial for pathogen recognition by host immunity and thus under various selection constraints. We focused on the interaction of drift and selection in TLR1B, TLR4, and TLR15 across 12 size-variable insular populations and compared them with the mainland population of the northern mockingbird (Mimus polyglottos), aiming to test if population size impacts selection efficiency. Nucleotide diversity positively correlated with the island size indicating an increasing effect of genetic drift in small populations. Despite this pattern, functional TLR properties were largely conserved, presumably due to purifying selection opposing drift independently on the island size. The degree of protein conservatism differed between the loci with TLR15 being the least conserved. Island colonisation did not lead to relaxed selection or to local adaptations. Together with the invariable physicochemical properties of the TLR variants, these observations imply that drift did not outweigh purifying selection despite restricted population size.