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. Our models predict that the suitable niche of this bat has been progressively shrinking since the last glaciation period. This study highlights threats to tropical montane 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 assessments of threats to biodiversity under global change should adopt a holistic approach, simultaneously studying the effects of multiple threats across temporal scales based on genetic, ecological and geographic information.
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.
Human overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, particularly regarding highly vulnerable marine ecosystems. Although a large effort has been made to design Marine Protected Areas (MPAs) worldwide, it is still unclear how many species actually exist in these MPAs, what is the genetic connectivity between areas with different protective regimes, and what is their relative genetic diversity. We answer these questions using morphologically cryptic species of the genus Mugil that are sympatric in the largest MPA in the Tropical Southwestern marine province. Population structure analyses show the existence of five highly divergent species (FST > 0.855) and no genetic divergence between two estuaries with different protection status (FST = 0.005). Sympatric individuals are assigned to single clusters and show strong concordance among hundreds of independent gene trees, consistent with full reproductive isolation and no ancestral nor ongoing hybridization. Differences of genetic diversity within species suggest that effective population sizes differ up to two-fold, probably reflecting differences in the magnitude of population expansions during the evolutionary history of these species, rather than recent impact of fisheries. Together, our results suggest that designing MPAs with areas of integral protection in between areas where fisheries are permitted could be an effective way to manage cryptic species that cannot have species-specific quotas. More generally, this work shows a cost-efficient approach that is transferable to other marine or terrestrial organisms of special concern, helping to implement science-based regulations for management and conservation.
Non-indigenous Daphnia ‘pulex’ have been found in many lakes in New Zealand (NZ) in the past 20 years, suggesting a recent invasion. However, very little is known about the origin of invasive D. ‘pulex’, whether they are D. pulex or D. pulicaria, and whether they are obligately asexual clones or cyclical parthenogens. Furthermore, the source and time of arrival of the invasive genotype(s) are unclear. We address these questions by genomic sequencing Daphnia populations from 13 lakes on the South Island and one on the North Island, NZ. Based on ~24,000 monomorphic species-specific markers, the invasive Daphnia on the South Island were found to be D. pulicaria, while those on the North Island are D. pulex/ pulicaria hybrids. Both the South and North Island Daphnia are phylogenetically clustered with North American D. pulicaria/pulex, thereby suggesting their North American origins. We further found that the South Island Daphnia populations are fixed heterozygotes for nearly all bi-allelic sites in the nuclear genome and contain identical mitochondrial genomes, suggesting the origin and proliferation from a single founder clone, which we experimentally verified to be an obligate asexual. Estimates from molecular data imply a colonization time for the South Island populations of ~ 60 years ago, with a likely invasion route associated with the introduction of salmonids from North America. Key words： Daphnia pulex; Daphnia pulicaria; invasion; obligately asexual; hybridization
Hybridization between species is likely to be associated with a new ecological impact. However, in termites, reports of hybridization mostly focus on hybrid zones caused by species invasion or the development of initial-stage colonies. In this study, we combined microsatellite genotyping with mitochondrial DNA sequencing to investigate the hybridization and adaptive introgression between two sympatric, long-differentiated related termite species, Reticulitermes flaviceps and R. chinensis, in nature. Similar levels of mitochondrial and nuclear genetic diversity were found in R. flaviceps and R. chinensis. Asymmetric interspecific genetic differentiation was observed between mitochondrial and nuclear genes, with high genetic divergence found in mitochondrial DNA but low genetic divergence in nuclear genes. Our results indicated a lack of mitochondrial gene exchange in R. flaviceps and R. chinensis but unconstrained nuclear introgression between them. This asymmetric genetic differentiation between nuclear and cytoplasmic material strongly suggests that there is interspecific hybridization between R. flaviceps and R. chinensis in nature, which provides new insight into the dynamics of hybridization and its potential consequences for speciation in termites.
Tiny predators, especially like phytoseiid mites, often experience a host of threats or stresses by fluctuating environmental factors. Heat acclimation as a superior adaptation strategy critically enhances abilities for organisms to handle with changing climate, but little is known about the molecular mechanism determining tolerant plastic responses in Phytoseiid mites. The relative expression of four identified HSP70 genes in two strains of Neoseiulus barkeri increased within a short time in temperature ramping treatment; meanwhile the expression of NbHSP70-1 and NbHSP70-2 in the conventional strain (CS) sharply decreased after 4 h displaying distinct contrast with the stable expression in the high-temperature adapted strain (HTAS). Western blot analysis showed that the protein level of NbHSP70-1 in CS was dramatically elevated at 0.5 h and decreased at 6 h at 42°C. Conversely, in HTAS, NbHSP70-1 was constantly induced and peaked at 6 h changed at 42°C. Furthermore, HSP70 suppression by RNAi knockdown had a greater influence on the survival of HTAS, causing a higher mortality under high temperature than CS. The recombinant certain exogenous NbHSP70-1 protein enhanced the viability of E. coli BL21 under lethal temperature of 50°C. These results suggested that HSP70 genes were a prominent contributor promoting the thermotolerance to heat stress and plastic change of HSP70 genes conferred the thermotolerance of HTAS through long-term heat acclimation. The divergent constitutive regulation of HSP70 to thermal is conducive to the flexible adaptability of predators in higher trophic level to trade off under extremely adversity stress.
Sexual dimorphism of plumage color is common in avians. A well-known example is mallard, in which drakes exhibit green head feathers, while females exhibit dull head feather color. Through microscopy observations, melanin was observed to be continuously deposited in feather barbules and to form a two-dimensional hexagonal lattice, which conferred the green feather coloration of drakes. Additionally, transcriptome analysis revealed that most pigmentation genes were highly expressed in feather follicles during the development of green feathers, which may contribute to melanin deposition. We identified 18 consensus differentially expressed genes in feather follicles by comparing the transcriptome differences in the male head vs. female head, male head vs. male back, and male head in the 7th week vs. male head in the 11th week. Among these genes, TYRP1 located on Z-chromosome of the mallard genome, showed an increasing trend in the feather follicles of drake heads during green feather development. In particular, its expression was 256 and 32 times higher in the head follicles of males than in those of the female head and the male back, respectively. Hence, the green feathers were determined by TYRP1 through sex-biased expression, which is common for genes linked with Z-chromosome in avians. The differential expression of TYRP1 in different body parts of males and among different time points may be due to differences in cis-regulation by transcription factors. We also demonstrated that the beautiful feather color of other male avians is largely caused by the sex-biased expression of pigmentation genes linked with Z-chromosome.
The symbiotic bacteria associated with honeybee gut have likely transformed from a free-living or parasitic lifestyle, through a close evolutionary association with the insect host. However, little is known about the genomic mechanism underlying bacterial transition to exclusive adaptation to the bee gut. Here we compared the genomes of bee gut symbionts Apibacter with their close relatives living in different lifestyles. We found that despite of general reduction in the Apibacter genome, genes involved in amino acid synthesis and monosaccharide detoxification were retained, which was likely beneficial to the host. Interestingly, the microaerobic Apibacter species have specifically preserved the NAR operon encoding for the nitrate respiration pathway which in contrast, is absent from the related non-free-living microaerobic pathogenic relatives. The NAR operon is also conserved in the cohabiting bee microbe Snodgrasella, but with a differed structure. This convergence implies a crucial role of respiration nitrate reduction for microaerophilic microbiomes to colonize bee gut epithelium. Genes involved in lipid, histidine and phenylacetate degradation are partially lost in Apibacter, possibly associated with the loss of pathogenicity. Antibiotic resistance genes were only sporadically distributed among Apibacter species, but condensed in their pathogenic relatives. Collectively, this study advanced our understanding of genomic transition underlying specialization in bee gut symbionts.
Populations with higher genetic diversity and larger effective sizes have greater evolutionary capacity (i.e., higher adaptive potential) to respond to ecological stressors. We are interested in how the adaptive potential captured in protein-coding genes persists in small populations and how it fluctuates relative to overall genomic diversity. We analyzed individual whole genome sequences from different populations of Montezuma Quail (Cyrtonyx montezumae), a small ground-dwelling bird that is sustainably harvested in some portions of its range but is of conservation concern elsewhere. Our historical demographic results indicate that overall, Montezuma Quail populations in the U.S. exhibit low levels of genomic diversity due in large part to long-term declines in effective population sizes over nearly a million years. The smaller and more isolated Texas population is significantly more inbred than the large Arizona and the intermediate-sized New Mexico populations. The Texas gene pool has a significantly lower proportion of deleterious alleles than the Arizona gene pool, but also significantly more high-frequency deleterious alleles that, coupled with elevated inbreeding, elevate the realized genetic load in Texas. Our results highlight that although small, isolated populations can maintain adaptive potential (i.e., genic diversity can still be high), they are at higher risk of inbreeding depression as detrimental mutations rise in frequency due to drift and weakened purifying selection. Our study illustrates how population genomics can be used to proactively assess both neutral and adaptive aspects of contemporary genetic diversity in a conservation framework while simultaneously considering deeper demographic histories.
Cryptic taxa have often been observed in the form of host‐associated species that diverged as the result of adaptation to alternate host plants. Untangling cryptic diversity in species complexes that encompass invasive species is a mandatory task for pest management. Moreover, investigating the evolutionary history of a species complex may help to understand the drivers of their diversification. The mealybug Hypogeococcus pungens was believed to be a polyphagous species from South America and has been reported as a pest devastating native cacti in Puerto Rico, also threatening cactus diversity in the Caribbean and North America. There is neither certainty about the identity of the pest, nor the source population from South America. Recent studies pointed to substantial genetic differentiation among local populations, suggesting that H. pungens is a species complex. In this study, we used a combination of genome-wide SNPs and mtDNA variation to investigate species diversity within H. pungens sensu lato to establish host plant ranges of each one of the putative members of the complex, to evaluate whether the pattern of host plant association drove diversification in the species complex, and to determine the source population of the Puerto Rican cactus pest. Our results suggested that H. pungens comprises at least five different species, each one strongly associated with specific host plants. We also established that the Puerto Rican cactus pest derives from southeastern Brazilian mealybugs. This is an important achievement because it will help to design reliable strategies for biological control using natural enemies of the pest from its native range.
The relative roles of rivers and refugia in shaping the high levels of species diversity in tropical rainforests has been widely debated for decades. Only recently has it become possible to take an integrative approach to answer these questions with genomic sequencing and paleo-species distribution modeling. Here, we tested the predictions of the classic river, refuge, and river-refuge hypotheses on diversification in the arboreal West and Central African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, machine learning-based demographic model selection, species paleo-distribution range estimates, and climate stability modeling to conduct a comprehensive phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers, and divergence times ranging from the mid to late Miocene. Our demographic and migration analyses supported our interpretation that rivers have represented strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river-refuge hypotheses in favor of the river barrier hypothesis. This study highlights the complexity of diversification dynamics in the African tropics and the advantage of integrative approaches to studying speciation in tropical regions.
Terrestrial squamate reptiles from the Galápagos archipelago have limited gene flow among islands, providing an opportunity to test paleogeographic models. Previous work suggests that Pleistocene glaciations had a strong influence on the evolution of Galápagos’ land-locked vertebrates, such as lizards and snakes, by allowing dispersal and contact among populations from different islands or islets through land connections. One prediction of this model is that extant populations, despite being isolated at present, are genetically similar due to recent (Pleistocene) gene flow. Here we test this prediction with a simple comparative phylogeographic analysis of two sympatric lizards from Floreana island and surrounding islets. Based on two mitochondrial genes, we show that Floreana lava lizards (Microlophus grayii) and leaf-toed geckos (Phyllodactylus baurii) from Floreana Island are very similar genetically to conspecifics from Champion, an islet in the Floreana group that was connected to Floreana during Pleistocene glacial maxima. Moreover, they are significantly less similar to conspecifics from Gardner, an islet in the Floreana group that was not in contact with Floreana during Pleistocene glacial maxima. Thus, our results support the idea of Pleistocene glaciation-driven contact among populations from different islands in the Floreana cluster with no identifiable subsequent dispersal. These results also show that Floreana and Champion populations are part of the same evolutionary significant unit for both species, which might be at risk due to an upcoming invasive mammal eradication program in Floreana. Therefore, Champion represents a reasonable source for potential reintroductions of both lava lizards and leaf-toed geckos into Floreana.
The high genetic diversity of rear-edge refugia has been predicted to result from repeated retreats of species’ ranges to low latitudes during glacial periods in the course of Quaternary climate change. However, a few recent empirical studies of cold tolerant plants revealed an opposite pattern. We investigate whether current populations of the cold-adapted and range-restricted Bupleurum euphorbioides in the Baekdudaegan, South Korea and North Korea, could be interglacial refugia, and document how their rear-edge populations differ genetically from those of typical temperate species. Phylogeographic analysis and ecological niche modeling (ENM) were used. Genetic structure was analyzed using microsatellite markers and chloroplast DNA sequences. The congener B. longiradiatum was included as a typical temperate plant species. Despite having almost identical life history traits, these congeneric species exhibited contrasting patterns of genetic diversity. ENM revealed a wide range expansion along the Korean mountains to northern Far East Russia (Primorsky) during the Last Glacial Maximum, but not during the last interglacial. Thus, we hypothesize that B. euphorbioides retreated to refugia following maximum range contraction during interglacial periods. Unlike populations in the central region, the rear-edge populations were genetically impoverished and uniform, both within populations and in pooled regional populations. The rear-edge has endured at least one past interglacial, contributing to the species’ genetic diversity. We believe that such genetic variation in the cold-adapted B. euphorbioides gives it the necessary adaptations that will enable it to survive an upcoming favorable environment (the next glacial), unless there is artificial environmental change.
Immune tissue associated with the major histocompatibility complex (MHC) is widely present in vertebrates highly polymorphic gene cluster. However, available published data about how amphibians MHCI genes react to pathogen infections are very few. The present study reports MHCI molecule in Rana dybowskii, and its differential expression in immunologically relevant tissues post-infection with lipopolysaccharide (LPS). The results showed that cDNA sequence of MHCIα contained 1047bp nucleotides encoding putative 348 amino acids. The phylogenetic analysis exhibited its evolutionary conservation within amphibians and formed a different clade with vertebrates. Morover, quantitative reverse transcription PCR analyses demonstrated that the MHCI gene was transcribed in the seven tested tissues, and analysis of immunologically relevant tissues of MHCI gene from the infected Rana dybowskii exhibited differential transcriptional activities. The expression of MHCI in the heart, liver, spleen, lung, kidneys, skin and muscular reached peak levels at 72, 24, 48, 12, 12, 12 and 72h post-infection(hpi), respectively. These findings indicate that MHCI is an indispensable part of the immune system. This is one of the first studies to investigate MHCIα in Rana dybowskii and can provide the foundation for further study of the immune function of MHC molecules in anti-infection.
An underdeveloped but potentially valuable molecular method in ecology is the ability to quantify the frequency with which foraging pollinators carry different plant pollens. Thus far, DNA metabarcoding has only reliably identified the presence/absence of a plant species in a pollen sample, but not its relative abundance in a mixed sample. Here we use a system of four congeneric, co-flowering plants in the genus Clarkia and their bee pollinators to (1) develop a molecular method to quantify different Clarkia pollens found on foraging bees; and (2) determine if bee pollinators carry Clarkia pollens in predictable ways, based on knowledge of their foraging behaviors. We develop a molecular method we call quantitative amplicon sequencing (qAMPseq) which varies cycling number (20, 25, 30, and 35 cycles) in polymerase chain reaction (PCR), individually indexing the same samples in different cycle treatments, and sequencing the resulting amplicons. These values are used to approximate an amplification curve for each Clarkia species in each sample, similar to the approach of quantitative PCR, which can then be used to estimate the relative abundance of the different Clarkia species in the sample. Using this method, we determine that bee visitation behaviors are generally predictive of the pollens that bees carry while foraging. We also show that some bees carry multiple species of Clarkia at the same time, indicating that Clarkia likely compete via interspecific pollen transfer. In addition to adding a ‘missing link’ between bee visitation behavior and actual pollen transfer, we suggest qAMPseq as another molecular method to add to the developing molecular ecology and pollination biology toolbox.
Many salmonid species exist in highly structured and isolated populations, and are susceptible to habitat fragmentation and disturbances. Gila Trout (Oncorhynchus gilae) is a threatened species found in the Southwestern United States. Gila trout is managed to preserve remnant populations (i.e. lineages) distributed across a fragmented landscape. We evaluated genomic variation within and among remaining lineages of Gila Trout using RADseq to assess how drift and selection have structured populations using neutral and outlier loci. We also examined whether a signature of hybridization was evident in relict populations. Despite Gila Trout lineages being significantly differentiated and highly structured with low effective population sizes, we found that most lineages maintained genomic diversity and were potentially locally adapted. Hybridization with non-native Rainbow Trout (O. mykiss) was not detected in any lineage. Some lineages may have experienced recent population bottlenecks perhaps associated with mortality from drought and severe wildfires. Current management strategies should be reevaluated and adapted to better account for long-term effects of climate change. Specifically, we suggest reconnecting some populations via dendritic stream networks to facilitate natural dispersal in a metapopulation context. This would allow natural genetic mixing on the landscape and potentially increase adaptive potential. Furthermore, genetic rescue should be implemented to preserve integrity of the unique Spruce Creek lineage that is currently compromised by extremely low diversity.