Alexander S. Mikheyev's research while affiliated with Australian National University and other places

Publications (197)

Preprint
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Novel transmission routes can allow infectious diseases to spread, often with devastating consequences. Ectoparasitic varroa mites vector a diversity of RNA viruses and, having switched hosts from the eastern to western honey bees (Apis cerana to Apis mellifera). They provide an opportunity to explore how novel transmission routes shape disease epi...
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Background Vector-borne viral diseases threaten human and wildlife worldwide. Vectors are often viewed as a passive syringe injecting the virus. However, to survive, replicate and spread, viruses must manipulate vector biology. While most vector-borne viral research focuses on vectors transmitting a single virus, in reality, vectors often carry div...
Article
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Microbiomes can enhance the health, fitness and even evolutionary potential of their hosts. Many organisms propagate favorable microbiomes fully or partially via vertical transmission. In the long term, such co-propagation can lead to the evolution of specialized microbiomes and functional interdependencies with the host. However, microbiomes are v...
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The evolution of automixis - i.e., meiotic parthenogenesis - requires several features, including ploidy restoration after meiosis and maintenance of fertility. Characterizing the relative contribution of novel versus pre-existing genes and the similarities in their expression and sequence evolution is fundamental to understand the evolution of rep...
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The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selec...
Article
Due to their spatial isolation, oceanic islands are natural systems to study evolutionary divergence. The Ogasawara Islands belong to the most isolated archipelagos on Earth and are well‐known for their high terrestrial endemicity; however, less is known about the marine realm. Here, we analyse the degree of oceanographic isolation of the archipela...
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Insects have been key players in assessments of biodiversity impacts of anthropogenically-driven environmental change, including the evolutionary and ecological impacts of climate change. Populations of Edith's Checkerspot Butterfly (Euphydryas editha) adapt rapidly to diverse environmental conditions, with numerous high-impact studies documenting...
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Background Evolution can occur with surprising predictability when organisms face similar ecological challenges. For most traits, it is difficult to ascertain whether this occurs due to constraints imposed by the number of possible phenotypic solutions or because of parallel responses by shared genetic and regulatory architecture. Exceptionally, or...
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This work investigated host-microbiome interactions during a crucial developmental stage—the transition from larvae to adults, which is a challenge to both the insect host and its microbiome. Using the honey bee as a tractable model system, we showed that microbiome transfer after emergence overrides any variation in the larval microbiome in honey...
Preprint
Full-text available
Vector-borne viral diseases threaten human and wildlife worldwide. Vectors are often viewed as a passive syringe injecting the virus, however to survive, replicate and spread, viruses must manipulate vector biology. While most vector-borne viral research focuses on vectors transmitting a single virus, in reality vectors often carry diverse viruses....
Article
Host switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and also may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study them in real‐time, and thei...
Article
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Primeval populations replicating at high error rates required a mechanism to overcome the accumulation of mutations and information deterioration. Known strategies to overcome mutation pressures include RNA processivity, epistasis, selection, and quasispecies. We investigated the mechanism by which small molecular ribozyme populations can survive u...
Preprint
Host switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and also may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study their demographic parameter...
Preprint
Full-text available
Evolution can occur with surprising predictability when faced with similar ecological challenges. How and why this repeatability occurs remains a central question in evolutionary biology, but the complexity of most traits makes it challenging to answer. Reptiles and mammals independently evolved oral venoms that consist of proteinaceous cocktails w...
Article
Full-text available
Oral venom systems evolved multiple times in numerous vertebrates enabling the exploitation of unique predatory niches. Yet how and when they evolved remains poorly understood. Up to now, most research on venom evolution has focused strictly on the toxins. However, using toxins present in modern day animals to trace the origin of the venom system i...
Cover Page
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Vol. 19(3) April 2021. PLoS Biol 19(3): ev19.i03. https://doi.org/10.1371/image.pbio.v19.i03
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Early in the process of adaptive radiation, allopatric disruption of gene flow followed by ecological specialization is key for speciation; but, do adaptive radiations occur on small islands without internal geographical barriers? Island populations sometimes harbour polymorphism in ecological special-izations, but its significance remains unclear....
Preprint
Full-text available
Host switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study them in real time and their demo...
Preprint
Full-text available
The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selec...
Article
Full-text available
Due to their pluripotent nature and unlimited cell renewal, stem cells have been proposed as an ideal material for establishing long-term cnidarian cell cultures. However, the lack of unifying principles associated with "stemness" across the phylum complicates stem cells' identification and isolation. Here, we for the first time report gene express...
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Background The honey bee parasite, Varroa destructor , is a leading cause of honey bee population declines. In addition to being an obligate ectoparasitic mite, Varroa carries several viruses that infect honey bees and act as the proximal cause of colony collapses. Nevertheless, until recently, studies of Varroa have been limited by the paucity of...
Data
Supplementary information about the specimens used in this research, including location of voucher specimens and link to field photographs on Dryad: https://datadryad.org/stash/share/5atVNHU8tBYO3dsNkqqIOlQvlpg-xbd4XsyEV-5G9Sw
Preprint
Full-text available
Background The honey bee parasite, Varroa destructor , is the leading cause of global honey bee population declines. In addition to being an obligate ectoparasitic mite, Varroa carries several viruses that infect honey bees and act as the proximal causes of colony collapses. Yet, until recently, the study of Varroa has been limited by the availabil...
Preprint
Full-text available
Oral venom systems evolved multiple times in numerous vertebrates enabling exploitation of unique predatory niches. Yet how and when they evolved remains poorly understood. Up to now, most research on venom evolution has focussed strictly on the toxins. However, using toxins present in modern day animals to trace the origin of the venom system is d...
Preprint
Full-text available
Introductory paragraph Host switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study them in r...
Article
Stony corals (Scleractinia) form the basis for some of the most diverse ecosytems on Earth, but we have much to learn about their evolutionary history and systematic relationships. In order to improve our understanding of species in corals we here investigated phylogenetic relationships between morphologically defined species and genetic lineages i...
Article
Full-text available
Microbes ubiquitously inhabit animals and plants, often affecting their host’s phenotype. As a result, even in a constant genetic background, the host’s phenotype may evolve through indirect selection on the microbiome. ‘Microbiome engineering’ offers a promising novel approach for attaining desired host traits but has been attempted only a few tim...
Article
A basic expectation of evolution by natural selection is that species morphologies will adapt to their ecological niche. In social organisms, this may include selective pressure from the social environment. Many non-ant parasites of ant colonies are known to mimic the morphology of their host species, often in striking fashion [1, 2], indicating th...
Article
While ectoparasitic Varroa mites cause minimal damage to their co-evolved ancestral host, the eastern honey bee (Apis cerana), they devastate their novel host, the western honey bee (Apis mellifera). Over several decades, the host switch caused worldwide population collapses, threatening global food security. Varroa management strategies have focus...
Article
Full-text available
Key innovations provide ecological opportunity by enabling access to new resources, colonization of new environments, and are associated with adaptive radiation. The most well-known pattern associated with adaptive radiation is an early burst of phenotypic diversification. Venoms facilitate prey capture and are widely believed to be key innovations...
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The study of island community assembly has been fertile ground for developing and testing theoretical ideas in ecology and evolution. The eco‐evolutionary trajectory of lineages after colonization has been a particular interest, as this is a key component of understanding community assembly. In this system, existing ideas such as the taxon cycle po...
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Understanding how organisms adapt to extreme environments is fundamental and can provide insightful case studies for both evolutionary biology and climate-change biology. Here, we take advantage of the vast diversity of lifestyles in ants to identify genomic signatures of adaptation to extreme habitats such as high altitude. We hypothesised two par...
Article
Herbivores use a wide range of factors to choose their host, including their own physiological states, physical characteristics of plants and the degree of competition. Field observations of herbivores in their native habitats provide a means for simultaneously estimating the relative importance of these factors, but statistical analysis of all the...
Preprint
Full-text available
Over millennia, steppe nomadic tribes raided and sometimes overran settled Eurasian civilizations. Most polities formed by steppe nomads were ephemeral, making it difficult to ascertain their genetic roots or what present-day populations, if any, have descended from them. Exceptionally, the Khazar Khaganate controlled the trade artery between the B...
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In this study, we report the first complete mitochondrial genome sequence of the Aquatic Coralsnake Micrurus surinamensis. The mitochondrial genome lengthis 17,375 bp, comprising 13 protein-coding genes, 2 rRNA (12S and 16S) and 22 tRNA, as well as two typical control regions. Phylogenetic analysis based upon 13 protein-coding genes showed clusters...
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Island biodiversity has long fascinated biologists as it typically presents tractable systems for unpicking the eco‐evolutionary processes driving community assembly. In general, two recurring themes are of central theoretical interest. First, immigration, diversification, and extinction typically depend on island geographical properties (e.g. area...
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Queen pheromones are chemical signals that mediate reproductive division of labor in eusocial animals. Remarkably, queen pheromones are composed of identical or chemically similar compounds in some ants, wasps and bees, even though these taxa diverged >150MYA and evolved queens and workers independently. Here, we measure the transcriptomic conseque...
Preprint
Full-text available
While ectoparasitic Varroa mites cause minimal damage to their co-evolved ancestral host, the eastern honey bee (Apis cerana), they devastate their novel host, the western 20 honey bee (Apis mellifera). The host switch caused worldwide population collapses, threatening global food security. Varroa management strategies have focused on breeding for...
Preprint
Herbivores use a wide range of factors to choose their host, including their own physiological states, physical characteristics of plants, and the degree of competition. Field observations of herbivores in their native habitats provide a means for simultaneously estimating the relative importance of these factors, but statistical analysis of all th...
Article
Full-text available
Multispecies host-parasite evolution is common, but how parasites evolve after speciating remains poorly understood. Shared evolutionary history and physiology may propel species along similar evolutionary trajectories whereas pursuing different strategies can reduce competition. We test these scenarios in the economically important association bet...
Preprint
Full-text available
Microbes ubiquitously inhabit animals and plants, often affecting their host's phenotype. As a result, even in a constant genetic background, the host's phenotype may evolve through indirect selection on the microbiome. 'Microbiome engineering' offers a promising novel approach for attaining desired host traits but has been attempted only a few tim...
Preprint
Full-text available
Understanding how organisms adapt to extreme environment is important in terms of both evolutionary biology and climate-change biology. Despite this and the increased number of sequenced arthropod genomes, little effort has been made to understand how cold-tolerant animals evolve. In this study, we take advantage of the impressive diversity of life...
Article
Full-text available
Eusociality has convergently evolved multiple times, but the genomic basis of caste-based division of labor and degree to which independent origins of eusociality have utilized common genes remain largely unknown. Here we characterize caste-specific transcriptomic profiles across development and adult body segments from pharaoh ants (Monomorium pha...
Article
Full-text available
Traditional static publication formats make visualization, exploration, and sharing of massive phylogenetic trees difficult. A phylogenetic study often involves hundreds of taxa, and the resulting tree has to be split across multiple journal pages, or be shrunk onto one, which jeopardizes legibility. Furthermore, additional data layers, such as spe...
Article
Full-text available
Gene expression changes contribute to complex trait variations in both individuals and populations. However, the evolution of gene expression underlying complex traits over macroevolutionary timescales remains poorly understood. Snake venoms are proteinaceous cocktails where the expression of each toxin can be quantified and mapped to a distinct ge...
Article
Full-text available
Development is often strongly regulated by interactions among close relatives, but the underlying molecular mechanisms are largely unknown. In eusocial insects, interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes. Here, we begin to characterize the social interactome regulating ant lar...
Article
To explore landscape genomics at the range limit of an obligate mutualism, we use genotyping‐by‐sequencing (ddRADseq) to quantify population structure and the effect of host–symbiont interactions between the northernmost fungus‐farming leafcutter ant Atta texana and its two main types of cultivated fungus. Genome‐wide differentiation between ants a...
Article
Full-text available
Background The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first gene...
Preprint
Full-text available
Gene duplication is associated with the evolution of many novel biological functions at the molecular level. The dominant view, often referred to as “neofunctionalization”, states that duplications precede many novel gene functions by creating functionally redundant copies which are less constrained than singletons. However, numerous alternative mo...
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Parent-of-origin effects, whereby specific phenotypes are differentially inherited paternally or maternally, provide useful clues to better understand transgenerational effect transmission. Ancestral diet influences offspring phenotypes, including body composition and fitness. However, the specific role that mothers and fathers play in the transmis...
Article
Social insects provide systems for studying epigenetic regulation of phenotypes, particularly with respect to differentiation of reproductive and worker castes, which typically arise from a common genetic background. The role of gene expression in caste specialization has been extensively studied, but the role of DNA methylation remains controversi...
Preprint
Full-text available
Development is often strongly regulated by interactions among close relatives, but the underlying molecular mechanisms are largely unknown. In eusocial insects, interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes. Here, we begin to characterize the social interactome regulating ant lar...
Preprint
Multispecies host-parasite evolution is common, but how parasites evolve after speciating remains poorly understood. On one hand, their shared evolutionary history and physiology may propel them along similar evolutionary trajectories. Alternatively, they may pursue different strategies to reduce competition with each other. Here, we test these sce...
Preprint
Full-text available
Tracking large numbers of densely-arranged, interacting objects is challenging due to occlusions and the resulting complexity of possible trajectory combinations, as well as the sparsity of relevant, labeled datasets. Here we describe a novel technique of collective tracking in the model environment of a 2D honeybee hive in which sample colonies co...
Preprint
Sudden biotic pressures, such as those from novel diseases and pathogens, require populations to respond rapidly or face potential extinction. How this response process takes place remains poorly understood, particularly in natural environments. In this study we take advantage of unique decade-long data sets of two wild honey bee ( Apis mellifera )...
Preprint
Full-text available
Gene expression changes contribute to complex trait variations in both individuals and populations. However, how gene expression influences changes of complex traits over macroevolutionary timescales remains poorly understood. Being comprised of proteinaceous cocktails, snake venoms are unique in that the expression of each toxin can be quantified...
Preprint
Full-text available
To explore landscape genomics at the range limit of an obligate mutualism, we used genotyping-by-sequencing (ddRADseq) to quantify population structure and the effect of hostsymbiont interactions between the northernmost fungus-farming leafcutter ant Atta texana and its two main types of cultivated fungus. At local scales, genome-wide differentiati...
Preprint
Full-text available
Eusociality, characterized by caste-based division of labor, has convergently evolved multiple times. However, the genomic basis of caste and degree to which independent origins of eusociality have utilized common genes is largely unknown. To elucidate these issues, we characterized caste-specific transcriptomic profiles across development and adul...
Preprint
Full-text available
Background The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first gene...
Preprint
Full-text available
Eusociality, the ultimate level of social organization, requires reproductive division of labor, and a sophisticated system of communication to maintain societal homeostasis. Reproductive division of labor is maintained by physiological differences between reproductive and sterile castes, typically dictated by pheromonal queen fertility signals tha...
Article
Full-text available
Following publication of this paper, Dr. Daniel Dashevsky discovered to our chagrin, that the transcriptomic datasets uploaded to the DNA Databank of Japan (DDBJ) contained numerous complete 3FTx sequences that were not included in our paper.[...]
Preprint
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Ancestral exposures can influence phenotypic expression in subsequent generations, which influence diverse biological processes ranging from phenotypic plasticity to obesity. Currently, most transgenerational studies work under the assumption of transgenerational response stability and reproducibility through time and across exposure differences, r...
Article
From human crowds to cells in tissue, the detection and efficient tracking of multiple objects in dense configurations is an important and unsolved problem. In the past, limitations of image analysis have restricted studies of dense groups to tracking a single or subset of marked individuals, or to coarse-grained group-level dynamics, all of which...
Article
We dekaryotized the multinucleate fungus Leucocoprinus gongylophorus, a symbiotic fungus cultivated vegetatively by leafcutter ants as their food. To track genetic changes resulting from dekaryotization (elimination of some nuclei from the multinuclear population), we developed two multiplex microsatellite fingerprinting panels (15 loci total), the...
Article
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Leafcutter ants propagate co-evolving fungi for food. The nearly 50 species of leafcutter ants (Atta, Acromyrmex) range from Argentina to the USA, with the greatest species diversity in southern South America. We elucidate the biogeography of fungi cultivated by leafcutter ants using DNA-sequence and microsatellite-marker analyses of 474 cultivars...
Preprint
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We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 co...
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The Lord Howe Island stick insect, Dryococelus australis, was once common on the island but was driven to extinction after the arrival of ship rats in the early 20th century [1, 2]. It was thought to be extinct for decades, until a tiny population of similar-looking stick insects was discovered 20 km away, on the islet of Ball’s Pyramid, in 2001 [2...