Biology subjects

Gemmell, N. J.

Publications and source records attributed to Gemmell, N. J..

18 recordsLinked to original sources

bioRxiv2026

Temporal persistence of vertebrate airborne environmental DNA in a natural open-air setting

Airborne environmental DNA (eDNA) is a promising tool for detecting a wide range of terrestrial taxa, including threatened and invasive species, from trace genetic material shed into the air. Yet, application of this technique in species management is constrained by a limited understanding of airborne eDNA ecology, including temporal persistence of signals in open-air environments. We investigated the temporal persistence of airborne eDNA in a natural outdoor setting, using the invasive Bennetts wallaby Notamacropus rufogriseus as a case study. We captured airborne eDNA from a single Bennetts wallaby carcass, deployed in an area where wallabies are otherwise not present. A total of 180 samples were collected, spanning the period before deploying the carcass, the 11 days it was on site, and for 32 days after its removal, at distances of 1, 10, and 100 metres using both active (fan-assisted) and passive (no fan) collection methods. Although overall detection rates were low, wallaby DNA was detectable up to 100 metres away shortly after the wallaby was introduced to the site and for up to three days after its removal. These findings indicate that airborne eDNA persists only briefly. Actively sampling air using battery-powered fans significantly improved detection rates relative to passive sampling. We demonstrate that airborne eDNA can detect individual organisms in outdoor environments, but reliable detection requires robust sampling and replication to capture rare, transient signals. By revealing how these signals persist over time, our findings provide a framework for optimizing field deployment and for distinguishing remnant DNA from new incursions.

molecular biology↗

bioRxiv2026

Loser effects orchestrate dominance hierarchies in socially-controlled sex change

Socially-controlled sex changing fishes provide powerful model systems for investigating sexual development and phenotypic plasticity in both behavior and physiology. The remarkable sexual transformation these fishes undertake is strongly influenced by their position in dominance hierarchies. However, the behavioral mechanisms underlying hierarchical formation remain understudied, particularly among female groups. Here, we investigated the role of winner-loser effects among females in establishing social dominance in a female-to-male sex changing fish. Individuals with prior losing experiences were more likely to lose subsequent size-matched fights, demonstrating clear loser effects, while there was no evidence for winner effects. Initial mirror aggression and some prior fighting behaviors, particularly submission, significantly and positively correlated with aggression in size-matched fights and subsequent mirror aggression; however, contest outcomes were not altered by these factors. Additionally, mirror aggression increased significantly only in subjects that drew size-matched fights. These findings demonstrate complex fighting dynamics in female-female competition and confirm the presence of loser effects in a sequential hermaphroditic species. These effects may represent evolutionarily advantageous mechanisms underlying sex change, thereby offering further context for examining how social rank advantages drive sexual transition.

animal behavior and cognition↗

bioRxiv2024

Behavioral and neural correlates of social hierarchy formation in a sex-changing fish

Social hierarchies in sex-changing fish determine which fish will change sex, yet the complexities of hierarchy formation at the neurobehavioral level are still being unraveled. Here, we investigate the formation of social hierarchies within groups of New Zealand spotty wrasse, integrating behavioral observations with neural activation patterns upon social disruption. We find that dominance hierarchies form linearly based on size, with larger fish displaying more dominant behaviors and smaller fish displaying more submissive behaviors. Disruption of the social hierarchy induced rapid behavioral changes, particularly in second-ranked fish, highlighting that second-ranked fish will opportunistically adopt a dominant position. Analysis of neural activation patterns reveals that the social decision-making network is deeply involved in the establishment of dominance, with the fish attaining dominance showing significant differences to all other ranked fish. Overall, this study underscores the complexity of social relationships and their neural underpinnings in the spotty wrasse, providing a foundation for further research into the cellular and molecular mechanisms of socially-controlled sex change, and demonstrates that disruption of the social hierarchy triggers rapid changes in both behavior and the social decision-making regions of the brain.

animal behavior and cognition↗

bioRxiv2024

A Cry For Kelp: Evidence for Polyphenolic Inhibition of Oxford Nanopore Sequencing of Brown Algae

Genomic resources for macroalgae are increasingly important for conservation and commercial management, however the generation of such resources continues to be hampered by difficulties in the isolation of suitable DNA. Even when DNA has been isolated that otherwise appears high quality, such samples may not perform well during the sequencing process. We here compare Oxford Nanopore long-read sequencing results for three species of macroalgae to those of non-macroalgal species and find that macroalgal samples tend to lead to rapid decline in the number of available sequencing pores resulting in reduced sequencing yield. LC-MS analysis of macroalgal DNA that would be considered suitable for sequencing reveals that DNA derived from dried macroalgae is enriched for polyphenol-DNA adducts - which may lead to sequencing inhibition. Our findings have wide-ranging implications for the generation of genomic resources from macroalgae, for example long read sequencing of dried herbarium specimens, and suggest a need to use fresh tissue wherever possible for genome sequencing.

molecular biology↗

bioRxiv2023

Whole genome assembly and annotation of the clover root weevil (Sitona obsoletus) using a combination of Illumina, 10X Genomics and MinION sequencing

Weevils are a highly diversified taxon, comprising about 70,000 described species that include many agricultural pests, biological control agents, and nutrient recyclers. Despite their importance and vast diversity, the number of sequenced genomes for the weevil family is still low (n=15). Here, we present a high-quality and contiguous genome assembly of Sitona obsoletus (Coleoptera: Curculionidae: Entiminae), a widespread invasive forage pest that infests clover species (Trifolium spp.) worldwide. We sequenced, assembled, and annotated the S. obsoletus genome using a hybrid approach that employed Nanopore long reads, 10X Chromium linked reads, Illumina short reads for assembly, and mRNA short read sequencing of various developmental stages for annotation. Our final annotated genome has a size of 1.2 Gb, with an N50 length of 313.85 kb. Benchmarking analyses against conserved single-copy Orthologs (BUSCO) found that over 94% of the genes were complete from each of the three BUSCO databases (Eukaryota, Insecta, and Arthropoda). A total of 9,777 protein-coding genes were annotated using the MAKER2 pipeline, of which 65% were functionally annotated. The annotated repeat elements make up 84.26% of the genome. The high-quality annotated genome of the weevil will facilitate a wide range of genetic, genomic, and phylogenetic studies on invasive weevils, as well as other weevil species in the subfamily Entiminae.

genomics↗

bioRxiv2023

The ghost of selection past: evolution and conservation relevance of the kakapo color polymorphism

The information contained in population genomic data can tell us much about the past ecology and evolution of species. We leveraged detailed phenotypic and genomic data of nearly all living k[a]k[a]p[o] to understand the evolution of its remarkable feather color polymorphism. The k[a]k[a]p[o] is an endangered and culturally significant parrot endemic to Aotearoa New Zealand, and the green and olive feather colorations are present at similar frequencies in the population. The presence of such a neatly balanced color polymorphism is remarkable because the entire population currently numbers less than 250 birds, which means it has been exposed to severe genetic drift. We dissected the color phenotype, demonstrating that the two colors differ in their light reflectance patterns due to differential feather structure. We used quantitative genomics methods to identify two genetic variants whose epistatic interaction can fully explain the species color phenotype. Our genomic forward simulations show that balancing selection might have been pivotal to establish the polymorphism in the ancestrally large population, and to maintain it during population declines that involved a severe bottleneck. We hypothesize that an extinct apex predator was the likely agent of balancing selection, making the color polymorphism in the k[a]k[a]p[o] a "ghost of selection past".

genomics↗

bioRxiv2023

A framework for identifying fertility gene targets for mammalian pest control

O_LIFertility-targeted gene drives have been proposed as an ethical genetic approach for managing wild populations of vertebrate pests for public health and conservation benefit. C_LIO_LIThis manuscript introduces a framework to identify and evaluate target gene suitability based on biological gene function, gene expression, and results from mouse knockout models. C_LIO_LIThis framework identified 16 genes essential for male fertility and 12 genes important for female fertility that may be feasible targets for mammalian gene drives and other non-drive genetic pest control technology. Further, a comparative genomics analysis demonstrates the conservation of the identified genes across several globally significant invasive mammals. C_LIO_LIIn addition to providing important considerations for identifying candidate genes, our framework and the genes identified in this study may have utility in developing additional pest control tools such as wildlife contraceptives. C_LI

genetics↗

bioRxiv2022

Non-invasive real-time genomic monitoring of the critically endangered kakapo

We used non-invasive real-time genomic approaches to monitor one of the last surviving populations of the critically endangered k[a]k[a]p[o] (Strigops habroptilus). We first established an environmental DNA metabarcoding protocol to identify the distribution of k[a]k[a]p[o] and other vertebrate species in a highly localized manner using soil samples. Harnessing real-time nanopore sequencing and the high-quality k[a]k[a]p[o] reference genome, we then extracted species-specific DNA from soil. We combined long read-based haplotype phasing with known individual genomic variation in the k[a]k[a]p[o] population to identify the presence of individuals, and confirmed these genomically informed predictions through detailed metadata on k[a]k[a]p[o] distributions. This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare species, potentially expanding the application of real-time environmental DNA research from monitoring species distribution to inferring fitness parameters such as genomic diversity and inbreeding.

genomics↗

bioRxiv2022

Genome assembly and annotation of the mermithid nematode Mermis nigrescens

Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. Lack of genomic resources has been a limiting factor for expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long-reads and 10X chromium link-reads. The assembly is 524 Mb in size consisting of 867 scaffolds. The N50 value is 2.42 Mb, and half of the assembly is in the 30 longest scaffolds. The assembly BUSCO score from the eukaryotic database (eukaryota_odb10) indicates that the genome is 86.7% complete and 5.1% partial. The genome has a high level of heterozygosity (6.6%) with a repeat content of 78.7%. mRNA-seq reads from different sized nematodes ([≤]2 cm, 3.5-7 cm, and >7 cm body length) representing different developmental stages were also generated and used for the genome annotation. Using ab initio and evidence-based gene model predictions, 12,313 protein-coding genes and 24,186 mRNAs were annotated. These genomic resources will help researchers investigate the various aspects of the biology and host-parasite interactions of mermithid nematodes.

genomics↗

bioRxiv2022

Whole genome assembly and annotation of the lucerne weevil Sitona discoideus

Weevils are a diverse insect group that includes many economically important invasive pest species. Despite their importance and diversity, only nine weevil genomes have been sequenced, representing a tiny fraction of this heterogeneous taxon. The genus Sitona consists of over 100 species, including Sitona discoideus (Coleoptera: Curculionidae: Entiminae), commonly known as lucerne (or alfalfa root) weevil. Sitona discoideus is an important pest of forage crops, particularly Medicago species. Using a dual sequencing approach with Oxford Nanopore MinION long-reads and 10x Genomics linked-read sequencing, we generated a high-quality hybrid genome assembly of S. discoideus. Benchmarks derived from evolutionarily informed expectations of gene content for near-universal single-copy orthologs comparison (BUSCO) scores are above 96% for single-copy orthologs derived from eukaryotes, arthropods, and insects. With a de novo repeat library, Repeatmasker annotated 81.45% of the genome as various repeat elements, of which 22.1% were unclassified. Using the MAKER2 pipeline, we annotated 10,008 protein-coding genes and 13,611 mRNAs. Furthermore, 68.84% of total predicted mRNAs and 67.90% of predicted proteins were functionally annotated to one or more of InterPro, gene ontology, and Pfam databases. This high-quality genome assembly and annotation will enable the development of critical novel genetic pest control technologies and act as an essential reference genome for broader population genetics and weevil comparative genetic studies.

genomics↗

bioRxiv2022

Environmental DNA reflects common haplotypic variation

Analysis of environmental DNA (eDNA) has gained widespread usage for taxonomically based biodiversity assessment. While interest in applying non-invasive eDNA monitoring for population genetic assessments has grown, its usage in this sphere remains limited. One barrier to uptake is that the effectiveness of eDNA detection below the species level remains to be determined for multiple species and environments. Here, we test the utility of this emergent technology in a population genetic framework using eDNA samples derived from water along New Zealands South Island (Otago Coast: n=9; Kaik[o]ura: n=7) and DNA obtained from tissue samples (n=76) of individual blackfoot p[a]ua (Haliotis iris) sampled from New Zealands Otago coast. We recovered four mitochondrial haplotypes from eDNA versus six from the tissue samples collected. Three common haplotypes were recovered with both eDNA and tissue samples, while only one out of three rare haplotypes - represented in tissue samples by one individual each - was recovered with our eDNA methods. We demonstrate that eDNA monitoring is an effective tool for recovering common genetic diversity from p[a]ua, although rare (< 5%) haplotypes are seldom recovered. Our results show the potential of eDNA to identify population-level haplotypes for gastropods in the marine environment identification below the species level and for studying the population genetic diversity of gastropods. This work supports eDNA methods as effective, non-invasive tools for genetic monitoring. Non-invasive eDNA sampling could minimize target organism stress and human interaction enabling population genetic research for hard-to-sample, delicate, or sensitive species.

genetics↗

bioRxiv2022

A high-quality genome assembly and annotation of the European earwig Forficula auricularia.

The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality and host-parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here we present a high-quality hybrid genome assembly for F. auricularia. The genome was assembled using nanopore long-reads and 10x chromium link-reads. The final assembly is 1.06Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ~90% from three sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. A phylogenetic analysis revealed the isolate used in our genomic analysis belongs to Subspecies B, one of the two known genetic subspecies of F. auricularia. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on Dermapterans.

genomics↗

bioRxiv2021

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Aquatic environmental DNA (eDNA) surveys are transforming how we monitor marine ecosystems. The time-consuming pre-processing step of active filtration, however, remains a bottleneck. Hence, new approaches omitting active filtration are in great demand. One exciting prospect is to use the filtering power of invertebrates to collect eDNA. While proof-of-concept has been achieved, comparative studies between aquatic and filter feeder eDNA signals are lacking. Here, we investigated the differences among four eDNA sources (water; bivalves; sponges; and ethanol in which filter-feeding organisms were stored) along a vertical transect in Doubtful Sound, New Zealand using three metabarcoding primers (fish (16S); MiFish-E/U). While concurrent SCUBA diver observations validated eDNA results, laboratory trials corroborated in-field bivalve eDNA detection results. Combined, eDNA sources detected 59 vertebrates, while divers observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was detected in ethanol, although only a reduced number of species were detected. Bivalves failed to reliably detect eDNA in both field and mesocosm experiments. While additional research into filter feeder eDNA accumulation efficiency is essential, our results provide strong evidence for the potential of incorporating sponges into eDNA surveys.

molecular biology↗

bioRxiv2020

Sex change in the New Zealand spotty wrasse (Notolabrus celidotus), a temperate model species

The stunning sexual transformation commonly triggered by age, size or social context in some fishes is one of the best examples of phenotypic plasticity thus far described. To date our understanding of this process is dominated by studies on a handful of subtropical and tropical teleosts, often in wild settings because sex change has been challenging to achieve in captivity. Here we have established the protogynous New Zealand spotty wrasse, Notolabrus celidotus, as a temperate model for the experimental investigation of sex change. Captive fish were induced to change sex using either aromatase inhibition or manipulation of social groups. Complete transition from female to male occurred over 60 days and time-series sampling was used to quantify changes in hormone production, gene expression and gonadal cellular anatomy using radioimmunoassay, nanoString nCounter mRNA and histological analyses, respectively. Early-stage decreases in plasma 17{beta}-estradiol (E2) concentrations or gonadal aromatase (cyp19a1a) expression were not detected in spotty wrasse, despite these being commonly associated with the onset of sex change in subtropical and tropical protogynous (female-to-male) hermaphrodites. In contrast, expression of the masculinising factor amh (anti-Mullerian hormone) increased during early sex change, implying a potential role as a proximate trigger for masculinisation. Expression of male-related genes responsible for androgen production cyp11c1 and hsd11b2 increased from mid sex change. Gonadal expression of the glucocorticoid and mineralocorticoid receptors nr3c1 and nr3c2, putative mediators of the stress hormone cortisol, increased in late stages of sex change. Collectively, these data provide a foundation for the spotty wrasse as a temperate teleost model to study sex change and cell fate in vertebrates. Summary statementThe spotty wrasse, Notolabrus celidotus, is a new temperate model for the study of vertebrate sex change, this work characterises endocrine and genetic markers based on laboratory induced sex change.

physiology↗

bioRxiv2020

A validation of Illumina EPIC array system with bisulfite-based amplicon sequencing

The Illumina Infinium(R) MethylationEPIC BeadChip system (hereafter EPIC array) is considered to be the current gold standard detection method for assessing DNA methylation at the genome-wide level. EPIC arrays are used for hypothesis generation or pilot studies, the natural conclusion is to validate methylation candidates and expand these in a larger cohort, in a targeted manner. As such, an accurate smaller-scale, targeted technique, that generates data at the individual CpG level that is equivalent to the EPIC array, is needed. Here, we tested an alternative DNA methylation detection technique, known as bisulfite-based amplicon sequencing (BSAS), to determine its ability to validate CpG sites detected in EPIC array studies. BSAS was able to detect differential DNA methylation at CpG sites to a degree which correlates highly with the EPIC array system. However, BSAS correlated less well with EPIC array data when the magnitude of change via EPIC array was greater than 5%, suggesting that this lower specificity at larger differential methylation values is a consequence of PCR amplification that BSAS requires. However, our data suggests that BSAS does offer advantages that the EPIC array: BSAS amplifies a region of the genome (~500bp) around a CpG of interest, allowing analyses of other CpGs in the region that may not be present on the EPIC array, aiding discovery of novel CpG sites and differentially methylated regions of interest. We conclude that BSAS offers a valid investigative tool for specific regions of the genome that are currently not contained on the array system.

genomics↗

bioRxiv2020

An in vitro ovarian explant culture system to examine sex change in a hermaphroditic fish

Many teleost fishes undergo natural sex change, and elucidating the physiological and molecular controls of this process offers unique opportunities not only to develop methods of controlling sex in aquaculture settings, but to better understand vertebrate sexual development more broadly. Induction of sex change in some sequentially hermaphroditic or gonochoristic fish can be achieved in vivo through social manipulation, inhibition of aromatase activity, and steroid treatment. However, the induction of sex change in vitro has been largely unexplored. In this study, we established an in vitro culture system for ovarian explants in serum-free medium for a model sequential hermaphrodite, the New Zealand spotty wrasse (Notolabrus celidotus). This culture technique enabled evaluating the effect of various treatments with 17β-estradiol (E2), 11-ketotestosterone (11KT) or cortisol (CORT) on spotty wrasse ovarian architecture for 21 days. A quantitative approach to measuring the degree of ovarian atresia within histological images was also developed, using pixel-based machine learning software. Ovarian atresia likely due to culture was observed across all treatments including no-hormone controls, but was minimised with treatment of at least 10 ng/mL E2. Neither 11KT nor CORT administration induced proliferation of spermatogonia (i.e. sex change) in the cultured ovaries indicating culture beyond 21 days may be needed to induce sex change in vitro. The in vitro gonadal culture and analysis systems established here enable future studies investigating the paracrine role of sex steroids, glucocorticoids and a variety of other factors during gonadal sex change in fish.Abbreviations11KT11-ketestosterone;Ccontrol (no steroid);D0day 0 reference tissues;CORTcortisol;E217β-estradiol;HDF5hierarchical data format 5;IPinitial phase;PVOprevitellogenic oocytes;TPterminal phase.View Full Text

zoology↗

bioRxiv2019

Genome-wide DNA methylation analysis of heavy cannabis use in a New Zealand longitudinal cohort

Cannabis use is of increasing public health interest globally. Here we examined the effect of cannabis use, with and without tobacco, on genome-wide DNA methylation in a longitudinal birth cohort (Christchurch Health and Development Study). We found the most differentially methylated sites in cannabis with tobacco users were in the AHRR and F2RL3 genes, replicating previous studies on the effects of tobacco. Cannabis-only users had no evidence of differential methylation in these genes, or at any other loci at the epigenomewide significance level (P<10-7). However, there were 521 sites differentially methylated at P<0.001 which were enriched for genes involved in cardiomyopathy and neuronal signalling. Further, the most differentially methylated loci were associated with genes with reported roles in brain function (e.g. TMEM190, MUC3L, CDC20 and SP9). We conclude that the effects of cannabis use on the mature human blood methylome differ from, and are less pronounced than, the effects of tobacco use, and that larger sample sizes are required to investigate this further.

genomics↗

bioRxiv2018

Stress, novel sex genes and epigenetic reprogramming orchestrate socially-controlled sex change

Bluehead wrasses undergo dramatic, socially-cued female to male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis. Our data suggest that the environmental stimulus is exerted via the stress axis, that repression of the aromatase gene (encoding the enzyme converting androgens to estrogens) triggers a cascaded collapse of feminizing gene expression, and identifies notable sex-specific gene neofunctionalization. Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals. These findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.\n\nOne Sentence SummaryOvary to testis transformation in a sex-changing fish involves transcriptomic and epigenomic reprogramming.

molecular biology↗