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

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Publications (208)


Fig. 3. A large proportion of the wild Dryococelus australis genome is covered by ROH of varying lengths, suggesting both recent and historical inbreeding. ROH length and coordinates estimated using bcftools v1.19-5-g2bbfdbf9 (Danecek et al. 2021). Multiple starting allele frequency values were used for bcftools indicated by the color legend. Different minimum length cutoffs are compared for each starting allele frequency.
Fig. 4. Recent demography has strongly depleted genetic diversity and increased inbreeding in Dryococelus australis. For all three panels, the outlier in the hybrid group is individual C01220. a) Population structure. Covariance matrix estimated using PCangsd v0.98 (Meisner and Albrechtsen 2018) with a minor allele frequency cutoff of 0.1 and eigenvectors calculated in R (R Core Team 2018). b) Autosomal heterozygosity calculated by estimating the single-sample site-frequency spectrum for each sample using the angsd -doSaf subroutine (Korneliussen et al. 2014) across all sites at 5 to 8X depth of coverage. See supplementary table S3, Supplementary Material online for raw values and comparison of estimates at 5 to 8X and 2 to 4X depth of coverage. c) Inbreeding coefficient calculated using the genome-wide probability of a position falling in an ROH estimated with the RZooRoH R package (Bertrand et al. 2019). The model presented here includes all samples for allele frequency estimation and K and R K values of 9 and 2.
Fig. 5. ROH estimated with the RZooRoH package (Bertrand et al. 2019) reflect recent and distant demography. The model presented here includes all samples for allele frequency estimation and K and R K values of 9 and 2. a) Predicted ROH on chromosome 6. Thin lines show the full length of the scaffold and thick lines demarcate the start and end positions of ROH. The black hashed box outlines a 15 Mbp region where hybrid individuals show a clear mixture of captive and wild haplotypes. b) Cumulative length (in log scale) and c) total number of ROH per individual across five length classes with black lines for group medians. In (b) and (c), the outlier to the hybrid group in the ">1 Mbp" length class is individual C01220.
Purging of Highly Deleterious Mutations Through an Extreme Bottleneck
  • Article
  • Full-text available

April 2025

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22 Reads

Molecular Biology and Evolution

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Rohan Cleave

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Kate Pearce

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[...]

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Alexander S Mikheyev

Transitions to captivity often produce population bottlenecks. On one hand, bottlenecks increase inbreeding and decrease effective population size, thus increasing extinction risk. On the other, elevated homozygosity associated with inbreeding may purge deleterious mutations. Previous empirical studies of purging in captive breeding programs have focused on phenotypic measurements. We test natural selection’s ability to purge deleterious mutations following an extreme population bottleneck by analysing patterns of genetic diversity in wild and captive-bred individuals of the Lord Howe Island stick insect, Dryococelus australis. Dryococelus australis has been bred in captivity for two decades, having passed through an extreme bottleneck – only two mating pairs with few new additions since then. The magnitude of the bottleneck together with high female fecundity but low offspring recruitment set up nearly ideal conditions for the purging of deleterious mutations. As expected, captive-bred individuals had a greater number of long runs-of-homozygosity compared to wild individuals, implying strong inbreeding in captivity which would facilitate purging in homozygous regions. Stop-codon mutations were preferentially depleted in captivity compared to other mutations in coding and non-coding regions. The more deleterious a mutation was predicted to be, the more likely it was found outside of runs-of-homozygosity, implying that inbreeding facilitates the expression and thus removal of deleterious mutations, even after such an extreme bottleneck and under the benign conditions of captivity. These data implicate inbreeding and recessive deleterious mutation load in fitness variation among captive and wild D. australis.

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Unveiling the evolutionary history of European vipers and their venoms from a multi-omic approach

December 2024

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734 Reads

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1 Citation

Snake genomes attract significant attention from multiple disciplines, including medicine, drug bioprospection, and evolutionary biology, due to the unique features found in snakes, especially, the evolution of venom. However, genomic research within the family Viperidae has mostly focused to date on the subfamily Crotalinae, while overlooking Viperinae, the Old World vipers. Among Viperinae, European vipers (Vipera) have been the subject of extensive research because of their venoms, phylogeographic, and ecological diversification. Nevertheless, venom research in this group has been conducted using mostly proteomes alone, while phylogeography and systematics in the genus have relied on biased information from mitochondrial phylogenies. Here, we generated chromosome-level genome assemblies for three Vipera species and whole-genome sequencing data for 94 samples representing 15 Vipera taxa. This comprehensive dataset has enabled us to disentangle the phylogenomic relationships of this genus, affected by mito-nuclear discordance and pervaded by ancestral introgression. Population-level analyses in the Iberian Peninsula, where the three oldest lineages within Vipera meet, revealed signals of recent adaptive introgression between ecologically dissimilar species, whereas chromosomal rearrangements isolate species occupying similar niches. Finally, using transcriptomic and proteomic data, we characterized the Vipera toxin-encoding genes, in which opposing selective forces were unveiled as common drivers of the evolution of venom as an integrated phenotype.


Transcriptome of differential gene expression for the three RNAs groups: gnathosoma only (gnathosoma), mites without gnathosoma and forelegs (WB_minus), and mites with both the gnathosoma and forelegs (WB_plus). (A) A schematic diagram of a Varroa mite, dorsal view: marked with red arrows is the pair of forelegs and marked with blue are the gnathosoma. (B) Principal components analysis (PCA) of gene expression separated the samples by their groups. The values used for the analysis are based on the 2067 differentially expressed genes with threshold of FDR < 0.05 and log2FC greater than one or lower than minus one. (C) Heat map of the 13 differentially expressed genes between the WB_minus and WB_plus. Log2 of the normalized reads are displayed as the color scale with downregulated genes in purple and upregulated genes in yellow
(A) Heat map of the chemosensory related differentially expressed gene transcripts. 83 transcripts identified in eight chemosensory groups, in three RNAs comparisons: gnathosoma, mites without gnathosoma and forelegs (WB_minus), and mites with both the gnathosoma and forelegs (WB_plus). Log2 fold change of the normalized reads are displayed at the bottom of the heat map, in colour scale (highest value = 15, lowest value = -2). Black asterisks “*”, “**”, “***” indicate significantly upregulated genes in the different comparisons (log2 fold change ≥ 1; Padj ≤ 0.05, 0.001, 0.0001); “#” indicates those that were close to significance (log2 fold change ≥ 1; Padj =  0.05; and “NF” indicate new transcripts detected in this study that was not previously reported by (Eliash et al. 2019) in the transcriptomes of the forelegs and rear legs of Varroa. Purple asterisks “*”, “**”, “***” indicate significantly downregulated genes in the different comparisons (log2 fold change ≤ -1; Padj ≤ 0.05, 0.001, 0.0001). (B) Twenty-one proteins identified in the proteome of the gnathosoma. Average intensity ratios are displayed at the bottom of the heat map, in colour scale (highest value = 70, lowest value = 0). OBPs (odorant-binding proteins); NPC2 (Niemann-Pick type C2 protein); IGRs (ionotropic glutamate receptors); IRs (ionotropic receptors); GRs (gustatory receptors); SNMPs (sensory neuron membrane proteins); TRPs (transient receptor potential proteins); ENaCs (degenerin/epithelial Na+ channel proteins)
Chemosensory function of Varroa gnathosoma: transcriptomic and proteomic analyses

October 2024

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105 Reads

Experimental and Applied Acarology

In this study, we evaluated the role of the gnathosoma (mouthparts) in chemosensing of the most devastating honey bee parasite, Varroa destructor mite. Through transcriptomic analysis, we compared the expression of putative chemosensory genes between the body parts containing the main chemosensory organs (the forelegs), gnathosoma and the rest of the body devoid of these two body parts. Furthermore, we checked the presence of chemosensory-related transcripts in the proteome of the gnathosoma. Our comparative transcriptomic analysis revealed the presence of 83 transcripts with known characteristic conserved domains belonging to eight chemosensory gene families in the three Varroa transcriptomes. Among these transcripts, 11 were significantly upregulated in the mite’s forelegs, compared to 8 and 10 in the gnathosoma and body devoid of both organs, respectively. Whilst the gnathosoma and the forelegs share similar expression of some putative lipid carrier proteins, membrane-bound receptors, and associated proteins, they also differ in the expression profiles of some transcripts belonging to these protein families. This suggests two functional chemosensory organs that may differ in their chemosensory function according to specific characteristics of compounds they detect. Moreover, the higher expression of some chemosensory transcripts in the body devoid of forelegs and gnathosoma compared to the gnathosoma alone, may suggest the presence of additional function of these transcripts or alternatively presence of additional external or internal chemosensory organs. Insights into the functional annotation of a highly expressed gustatory receptor present in both organs using RNA interference (RNAi) are also revealed.


Figure 4. Runs-of-homozygosity estimated with the RZooRoH package (Bertrand et al., 2019) reflect recent and
Purging of highly deleterious alleles through an extreme bottleneck

July 2024

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97 Reads

Transitions to captivity are usually population bottlenecks and so may contribute to the fitness decline of captive-bred species by genetic drift and increased inbreeding. Purging can remove deleterious alleles from populations during declines and bottlenecks but the strength of this effect across different scenarios is unknown. The Lord Howe Island stick insect, Dryococelus australis, has been bred in captivity since 2003 and passed through an extreme bottleneck: only two mating pairs with only one new addition since then. We document extremely low heterozygosity and high inbreeding in the wild, suggestive of low population size and/or a recent colonisation bottleneck. We then test the ability of natural selection to purge deleterious alleles following an extreme population bottleneck by comparing patterns of genetic diversity in wild and captive-bred D. australis. Captive-bred individuals had lower heterozygosity and a greater number of long runs-of-homozygosity compared to wild individuals, implying strong inbreeding in captivity which would facilitate purging. Highly deleterious alleles were preferentially depleted in captivity but all other alleles, coding and non-coding, had the same mean frequency change in captivity compared to the wild. The more deleterious an allele was predicted to be, the more likely it was found outside of runs-of-homozygosity. These results are consistent with inbreeding purging these deleterious alleles. We show that purging can operate on highly deleterious alleles via inbreeding, even after an extreme bottleneck. This may contribute to the persistence of captive populations, although strong drift will also limit their adaptive potential in the future, in captivity and once reintroduced into the wild.


Varroa mites escape the evolutionary trap of haplodiploidy

May 2024

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222 Reads

Genetic diversity is essential for populations adapting to environmental changes. Due to genetic bottlenecks invasive species often have reduced genetic diversity. However, they must quickly adapt to changes in new environments, potentially including anthropogenic countermeasures. This paradox raises a fundamental question: how do species adapt to changes while having low genetic diversity? This tension is more pronounced for some species, for example parasites go through additional bottlenecks between hosts and haplodiploid species have a lower effective population size, as males can inherit and transmit only half of their mother’s genome. To investigate how species with such traits reconcile diversity and adaptability, we examined inheritance in the Varroa mite ( Varroa destructor ), a well-studied invasive parasite of honey bees fitting all of the above criteria. By following the flow of alleles across three-generation pedigrees we found that Varroa, so far believed to be haplodiploid, is actually not. Rather, it has a unique reproductive system in which females clonally produce functionally diploid sons. While males lose somatic DNA during development, they can transmit either maternal allele to their daughters with equal probability. Modeling shows Varroa loses heterozygosity slower under typical sib-mating conditions, relative to haplodiploidy. This permits a greater effective population size relative to a purely haplodiploid system and increased evolutionary potential. This reversion to diploidy is a singular example of escaping the ‘evolutionary trap’ of haplodiploidy, which is believed to be an evolutionary stable end state. Plasticity in reproductive systems could be more common than assumed, and may potentially explain the remarkable resilience and high adaptivity of Varroa and other invasive parasites. Significance Varroa mites have driven the collapse of honey bee populations since their worldwide spread in the middle of the 20th century. Despite repeated genetic bottlenecks, Varroa has adapted to diverse environments and has overcome many pesticides. Using pedigree analysis, we found that Varroa re-evolved diplodiploid reproduction from an evolutionary history of haplodiploidy. Diplodiploidy permits a higher effective population size and evolutionary potential, likely facilitating Varroa’s ongoing success. Females produce males clonally, passing on their entire genomes. Varroa is a singular exception to the theoretically and empirically observed rule that, once evolved, haplodiploidy is an evolutionarily stable end state (an ‘evolutionary trap’). Novel mechanistic studies of even well-known organisms can lead to surprising insights into the evolutionary plasticity of reproductive systems.


Parthenogenetic Stick Insects Exhibit Signatures of Preservation in the Molecular Architecture of Male Reproduction

April 2024

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52 Reads

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3 Citations

Genome Biology and Evolution

After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (1) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (2) that gene co-expression network architecture could constrain individual gene expression. Our testing ground has been the Bacillus stick insect species complex, which contains close relatives that are either bisexual or parthenogenetic. After the identification of genes expressed in male reproductive tissues in a bisexual species, we investigated their gene co-expression network structure in two parthenogenetic species. We found that gene co-expression within the male gonads was partially preserved in parthenogens. Furthermore, parthenogens did not show relaxed selection on genes upregulated in male gonads in the bisexual species. As these genes were mostly expressed in female gonads, this preservation could be driven by pleiotropic interactions and an ongoing role in female reproduction. Connectivity within the network also played a key role, with highly connected - and more pleiotropic - genes within male gonad also having a gonad-biased expression in parthenogens. Our findings provide novel insight into the mechanisms which could underlie the production of rare males in parthenogenetic lineages; more generally, they provide an example of the cryptic persistence of a lost trait molecular architecture, driven by gene pleiotropy on other traits and within their co-expression network.


SCN1B sequences showing the positively selected G33N substitution in T. rubripes and the location of the residue on the protein (in red).
Crystal structure of the human Nav1.4 VGSC (orange) in complex with subunit β1 (cyan). TM = Transmembrane domain, Ig = Immunoglobulin domain. Residue G33 (mutated to N33 in the TTX-resistant T. rubripes) is highlighted in red. Structure retrieved from the Protein Data Bank following Pan et al. [15].
SCN2B sequences showing the positively selected P35X substitution in TTX-resistant taxa and E. electricus and the location of the residue on the protein (in red).
SCN3B sequences showing the positively selected Q93X and D197X substitutions in TTX-resistant taxa as well as P. textilis and D. rerio. The location of the residues on the protein is highlighted in red.
List of species whose SCNB sequences were used in this study.
Sodium Channel β Subunits—An Additional Element in Animal Tetrodotoxin Resistance?

January 2024

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98 Reads

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3 Citations

Tetrodotoxin (TTX) is a neurotoxic molecule used by many animals for defense and/or predation, as well as an important biomedical tool. Its ubiquity as a defensive agent has led to repeated independent evolution of tetrodotoxin resistance in animals. TTX binds to voltage-gated sodium channels (VGSC) consisting of α and β subunits. Virtually all studies investigating the mechanisms behind TTX resistance have focused on the α subunit of voltage-gated sodium channels, where tetrodotoxin binds. However, the possibility of β subunits also contributing to tetrodotoxin resistance was never explored, though these subunits act in concert. In this study, we present preliminary evidence suggesting a potential role of β subunits in the evolution of TTX resistance. We gathered mRNA sequences for all β subunit types found in vertebrates across 12 species (three TTX-resistant and nine TTX-sensitive) and tested for signatures of positive selection with a maximum likelihood approach. Our results revealed several sites experiencing positive selection in TTX-resistant taxa, though none were exclusive to those species in subunit β1, which forms a complex with the main physiological target of TTX (VGSC Nav1.4). While experimental data validating these findings would be necessary, this work suggests that deeper investigation into β subunits as potential players in tetrodotoxin resistance may be worthwhile.


The molecular groundplan of male reproduction is partially preserved in parthenogenetic stick insects

November 2023

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44 Reads

After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (1) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (2) that gene co-expression network architecture could constrain individual gene expression. Our testing ground has been the Bacillus stick insect species complex, which contains close relatives that are either bisexual or parthenogenetic. After the identification of genes expressed in male reproductive tissues in a bisexual species, we investigated their gene co-expression network structure in two parthenogenetic species. We found that gene co-expression within the male gonads was preserved in parthenogens. Furthermore, parthenogens did not show relaxed selection on genes upregulated in male gonads in the bisexual species. As these genes were mostly expressed in female gonads, this preservation could be driven by pleiotropic interactions and an ongoing role in female reproduction. Connectivity within the network also played a key role, with highly connected - and more pleiotropic - genes within male gonad also having a gonad-biased expression in parthenogens. Our findings provide novel insight into the mechanisms which could underlie the production of rare males in parthenogenetic lineages; more generally, they provide an example of the cryptic persistence of a lost trait molecular ground plan, driven by gene pleiotropy on other traits and within their co-expression network. Significance Loss of traits commonly occurs in diverse lineages of organisms. Here we investigate what happens to genes and regulatory networks associated with these traits, using parthenogenetic insect species as a model. We investigated the fate of genes and gene regulatory networks associated with male gonads in a bisexual species in closely related parthenogens. Rather than showing signs of disuse and decay, they have been partially preserved in parthenogens. More highly pleiotropic genes in male gonads were more likely to have a gonad-biased expression profile in parthenogens. These results highlight the role of pleiotropy in the cryptic persistence of a trait molecular ground plan, despite its phenotypical absence.


Systematics of the Ogyris aenone (Waterhouse, 1902) complex (Lepidoptera: Lycaenidae): threatened Australian butterflies of national conservation significance

July 2023

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337 Reads

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2 Citations

The butterfly genus Ogyris Angas, 1847 consists of several striking but poorly resolved complexes endemic to Australia and New Guinea, many of which have an obligate association with ants. Here, we revise the systematics of the Ogyris aenone (Waterhouse, 1902) complex through an integrative taxonomic approach based on molecular phylogenetic analysis, morphological examination, life histories and ecology. Mitochondrial sequence data based on concatenated cytochrome oxidase I (COI) and cytochrome b (cytb) (total of 1203 bp) for 36 ingroup samples were generated and combined with sequences available on NCBI GenBank for Ogyris. Phylogenetic analysis inferred by maximum likelihood methods resolved five taxa within this group, with one taxon, Ogyris caelestia Beaver & Braby sp. nov., described as a new species and another, O. doddistat. rev., raised to full species. Phylogenetic relationships among the five taxa are as follows: (O. caelestia + O. aenone) + (O. ianthis + (O. iphis + O. doddi)). This revision brings the number of recognised Ogyris species to 16 and for the tribe Ogyrini to 18. This group of butterflies was found to be scarce – field samples of host trees that had the co-occurrence of both mistletoe and the appropriate attendant ant at 12 locations in eastern and northern Australia revealed low rates of occupancy (<50%, with an overall average of 17%) based on the presence of immature stages of the five butterfly species. The complete life histories, general biology and ecology of all members of this species-group are illustrated and diagnosed for the first time and confusing aspects of the literature are clarified. Several taxa are of conservation significance, including the new species, and future directions are discussed in relation to this. ZooBank: urn:lsid:zoobank.org:pub:FC258ED6-AA1F-4E11-BFE1-D0A612E4F166


Evolutionarily diverse origins of deformed wing viruses in western honey bees

June 2023

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431 Reads

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15 Citations

Proceedings of the National Academy of Sciences

Novel transmission routes can allow infectious diseases to spread, often with devastating consequences. Ectoparasitic varroa mites vector a diversity of RNA viruses, 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 epidemiology. As the principal driver of the spread of deformed wing viruses (mainly DWV-A and DWV-B), varroa infestation has also driven global honey bee health declines. The more virulent DWV-B strain has been replacing the original DWV-A strain in many regions over the past two decades. Yet, how these viruses originated and spread remains poorly understood. Here, we use a phylogeographic analysis based on whole-genome data to reconstruct the origins and demography of DWV spread. We found that, rather than reemerging in western honey bees after varroa switched hosts, as suggested by previous work, DWV-A most likely originated in East Asia and spread in the mid-20th century. It also showed a massive population size expansion following the varroa host switch. By contrast, DWV-B was most likely acquired more recently from a source outside East Asia and appears absent from the original varroa host. These results highlight the dynamic nature of viral adaptation, whereby a vector's host switch can give rise to competing and increasingly virulent disease pandemics. The evolutionary novelty and rapid global spread of these host-virus interactions, together with observed spillover into other species, illustrate how increasing globalization poses urgent threats to biodiversity and food security.


Citations (59)


... Similar elimination of paternal genomes was observed in wasps [19] and arachnids [22]. Additionally, the whole paternal genome This includes the following genera: Ciliates: Paramecium [9], Tetrahymena [10], Oxytricha [10], Stylonychia [11], Euplotes [11]; Worms: Strongyloides [12], Oscheius [13], Ascaris [14], Parascaris [15]; Insects: Phragmatobia [8] (moths), Liposcelis 12 (booklice), Bacillus [16] (stick insects), Bradysia [17] and Sciara [8] (fungus gnats), Mayetiola [18] (hessian fly), Nasonia [19] (jewel wasp); Copepods: Cyclops [20], Mesocyclops [21]; Arachnids: Metaseiulus [22]; Jawless fish: Petromyzon [23] (lamprey), Myxine [24] (hagfish); Fish: Hydrolagus [25], Hypseleotris [26]; Amphibians: Pelophylax [27], Bufotes [28]; Songbirds: Taeniopygia [29] (zebra finch), Lonchura [30]; Mammals: Perameles [31] and Isoodon [32] (bandicoots), Acomys [33] (spiny mouse); Plants: Aegilops [34] (goat grass), Brachiaria [35], Hordeum [36]. ...

Reference:

Functions and mechanisms of eukaryotic RNA-guided programmed DNA elimination
Parthenogenetic Stick Insects Exhibit Signatures of Preservation in the Molecular Architecture of Male Reproduction
  • Citing Article
  • April 2024

Genome Biology and Evolution

... They complement each other: 6 J8I with a correct α but incorrect β, and 7 TJ8 with an incorrect α but a correct β3 subunit in the complex structure (see Table S1). Recently, the biochemical electrophysiological modulation of tetrodotoxin (TTX) and conotoxin as binders to Na v α/β complexes was reported [47][48][49][50][51]. Regulation of genes which express Na v 1.7 channels, along with β4, was studied in cancer-related health issues [52,53]. ...

Sodium Channel β Subunits—An Additional Element in Animal Tetrodotoxin Resistance?

... These genomes showed a high percentage of identity (96.5% to 97.8%) with the reference genome from the DWV-A from Italy (GenBank accession NC_004830), with a coverage of 100% in all cases. Phylogenetic analysis revealed that the seven Uruguayan sequences grouped closely with a DWV sequence from Argentina (GenBank accession OR597290) and with two DWV sequences obtained from Uruguayan V. destructor mites (Hasegawa et al. 2023). In contrast, they exhibited a distant relationship to a sequence originating from Chile (GenBank accession JQ413340, Figure 4), separately from the branches that contain the DWV-B and DWV-C sequences (GenBank accession NC_006494 and CEND01000001, respectively, Figure 4). ...

Evolutionarily diverse origins of deformed wing viruses in western honey bees

Proceedings of the National Academy of Sciences

... This includes a surveillance network of sentinel hives positioned at ports of entry that are frequently monitored for exotic bee pests and pathogens (Clifford et al. 2011). In June 2022, V. destructor was detected in biosecurity sentinel hives at the port of Newcastle on Australia's east coast (Chapman et al. 2023). While this gave relatively early detection of the incursion, epidemiological analysis indicated that mites had been in the local area undetected for at least 12 months (McFarlane et al. 2024). ...

The final frontier: ecological and evolutionary dynamics of a global parasite invasion

... Most viruses in this study show either a positive co-occurrence or correlation, a finding well-established in other studies (e.g., Cornman et al., 2012;D'Alvise et al., 2019). We would expect many honey bee viruses to co-occur and have correlated loads because many are transmitted or amplified by Varroa mite parasitism (Francis et al., 2013;Mondet et al., 2014;Eliash et al., 2022;Dobelmann et al., 2024). Although we could not assess Varroa infestation of the drones during their development, some were likely parasitized, presumably triggering higher loads of multiple viruses (Lamas et al., 2023). ...

Vector-virus interaction affects viral loads and co-occurrence

... Compounds from bacteria like Fusobacterium nucleatum and Enterobacteriaceae support inflammation and drive genomic instability within the CRC microenvironment [915][916][917]. Additionally, antibiotic or chemotherapy use can alter the microbiome composition and metabolite outputs through dysbiosis, potentially compromising treatment responses [918][919][920][921]. Modulation of the gut microbiome and its metabolic functions therefore presents opportunities to influence CRC metabolism and therapeutic response [907]. ...

Experimental inheritance of antibiotic acquired dysbiosis affects host phenotypes across generations

... However, increased adaptive selection acting on social species could have the same effect. RELAX analyses 35 suggest that the elevated dN/dS ratios in social species is almost entirely due to relaxed selection, as has previously been suggested 36 . We also show elevated dN/dS ratios on X chromosomes compared to autosomes across all branches in the phylogeny, except for the terminal branches of S. pacificus. ...

Genomic signatures of recent convergent transitions to social life in spiders

... Japan are strongly influenced by the Kuroshio Current that flows from the Ryukyus northward along the Pacific coast of Japan (Tsuchiya & Omori, 2004;Veron et al., 2015), while the Ogasawara Islands are removed from the region of influence of the Kuroshio Current ( Figure 1). This strong oceanographic isolation has been implied as a driver of the genetic differentiation of its coral populations, giving rise to its distinct Scleractinia coral populations (Wepfer et al., 2022). When compared to the two closest, roughly equidistant coral ecoregions, the corals of Ogasawara Islands are more diverse (186 species from 48 genera) than those of highlatitude mainland Japan (115 species from 44 genera), but less diverse compared to those of the Ryukyu Islands (402 species from 73 genera), with which they share a common latitudinal range and similar climatic conditions (Veron et al., 2023). ...

The oceanographic isolation of the Ogasawara Islands and genetic divergence in a reef‐building coral

... The evolution of 38 circadian genes may thus be involved in the divergence of temporal niches, therefore 39 enhancing pre-zygotic barrier to gene flow in sympatric species. Interestingly, in 40 Lepidoptera, some genes involved in the regulation of circadian behaviour are sex-linked: 41 for instance the gene Period, responsible for diurnal or nocturnal activity in some Panama, Veraguas district (GPS coordinates: 8.525869707300163, -81.13020529212375) 66 in July 2022 for M. granadensis and M. amathonte (Export permit number: 67 PA-01-ARB-076-2022) and in French Guiana, Roura district (GPS coordinates: 71 SNAP-frozen and kept at -80°C. 72 DNA extractions and genome sequencing 73 For genomic analyses, the DNA extraction was carried out from the thorax muscles 74 using the Qiagen Genomic-tip 100/G kit, following supplier instructions. ...

A Genome for Edith's Checkerspot Butterfly: An Insect with Complex Host-Adaptive Suites and Rapid Evolutionary Responses to Environmental Changes

Genome Biology and Evolution

... For example, the amplification, reverse transcription, and forward transcription steps of in vitro selection have been shown to influence sequence fitness. [27] These processes become more prevalent under less stringent selection conditions and when the population has reached a fitness plateau, as seen in R2 of both the G5 and A9 selections. [23] Conversely, the lenient conditions employed in the single-mutation selections (i. ...

Ribozyme Mutagenic Evolution: Mechanisms of Survival

Origins of Life and Evolution of Biospheres