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

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.

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.

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.

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.

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.

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.

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.

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.

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

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.