Biology subjects

Markee, A.

Publications and source records attributed to Markee, A..

10 recordsLinked to original sources

bioRxiv2026

Genomics and CT imaging reveal diversity in silk genes and gland morphology of webspinners

Webspinners (Insecta: Embioptera) are an unusual insect order that are known for their subsocial behavior and prolific silk-production. Due to their unique foreleg silk glands, and spider-like ability to produce silk throughout their entire life cycle, webspinners are hypothesized to have evolved silk independently from other arthropod lineages. To date, there are no reference-quality genomes available for the order, preventing the study of their silk gene origination and diversification. Here, we assembled PacBio HiFi reference genomes and characterized the silk genes present in two webspinner species, Aposthonia ceylonica and Oligotoma nigra. The genomes reveal multiple full-length copies of the primary Embioptera silk gene, e-fibroin, that have undergone both ancestral and recent gene duplications within the group. For both species, all e-fibroin paralogs show the presence of complex repeat units consisting of multiple exons and introns that are remarkably homogenized across each gene. We also used CT-scanning of the internal silk glands to provide details concerning the localization of silk production in foreleg tarsi, and interspecific morphology. Article summaryThis study introduces the first high-quality genomes for webspinners, enabling new research on silk for evolutionary biologists and materials scientists alike. The authors sequenced two embiopteran species, Aposthonia ceylonica and Oligotoma nigra, to compare silk genes and gland structure using micro-computed tomography, an imaging method that shows internal anatomy in detail. They found multiple copies of the primary silk gene in both species that likely arose from multiple duplication events at different evolutionary times. These silk genes exhibit unusual gene structure with hierarchically organized repeat units that are highly homogenized within a gene. The findings show that silk genes have a complex evolutionary history in webspinners and provide a foundation for studying silk diversity within the order, and in the broader context of insect silk.

evolutionary biology↗

bioRxiv2026

Leaving X: How scale insects evolved alternatives to chromosomal sex determination

Reproduction is a core feature of life, which makes understanding the reproductive diversity of organisms a fundamental goal of evolutionary biology. It is still unclear why sex determination systems are faithfully conserved for hundreds of millions of years in some taxa but repeatedly turn over in others. A prime example is the true bugs, Hemiptera. The vast majority of families employ a conserved X sex chromosomal system, but in scale insects (Coccomorpha), sex determination systems are far more varied. Different families may retain X chromosomes, employ a rare form of haplodiploidy known as paternal genome elimination (PGE), or forgo sexual reproduction in favor of simultaneous hermaphroditism. While these systems have been known for decades, only recently has non-model genomics enabled their study with modern bioinformatic methods. We collected and sequenced representatives of rare, early-diverging scale insects to study genomic changes that coincide with transitions between sex determination systems. Using ancillary expression data, we also explored sex-biased gene expression in a subset of scale insects on both sides of one transition. In a newly updated molecular phylogeny, we recovered two independent losses of X chromosomal sex determination, once in the family Monophlebidae and a second time at the base of the families that employ PGE. In the former, genomic rearrangements begin before the X is lost and any previously X-linked orthologs have been absorbed into one of two massive, shuffled autosomes in the hermaphrodites. In the latter, the X chromosome itself is faithfully preserved in early diverging PGE taxa; it appears to have merely lost its sex determination function. We analyze ortholog conservation across these transitions and find few genes lost, with only one orthogroup lost in both transitions, and a number of orthogroups gained, suggesting these large transitions did not require large changes to the gene content of the X chromosome. Expression data suggests that extreme sexual dimorphism of gene expression predates sex determination turnover and may have helped enable it. Together these new observations illustrate the multiple routes to sex determination turnover, help refine hypotheses for its causes, and provide a wealth of new resources for the modern genomic study of scale insects.

evolutionary biology↗

bioRxiv2025

Insights from the lack of an enigmatic trait: monomorphic sperm in evergreen bagworm moths and the evolution of sperm dimorphism

Reproductive traits contain some of the most bizarre and unintuitive innovations seen across the tree of life. Chief among these is the sperm dimorphism of butterflies and moths (Lepidoptera). Males make two types of sperm: traditional fertilizing sperm (eupyrene) and a second, non-fertilizing type (apyrene) that lacks a nucleus entirely. Despite decades of study, the function and evolution of this second sperm type has remained unclear. Here we explore the sperm biology of the evergreen bagworm moth, Thyridopteryx ephemeraeformis (Lepidoptera: Tineoidea: Psychidae), and find no evidence for non-fertilizing sperm in this species. We generate genomic, transcriptomic, and proteomic resources to characterize the apparently monomorphic sperm of this species and compare it to that of other Lepidoptera. The fertilizing sperm of the evergreen bagworm shows key differences from other studied species, especially a lack of proteolytic enzymes used to break down sperm bundles in other species. Combining this and other evidence, we offer new hypotheses for the evolution and function of this enigmatic reproductive trait. Notably, early diverging moths appear to produce far less non-fertilizing sperm in general than later diverging Lepidoptera. We infer that non-fertilizing sperm are not necessary in these taxa, perhaps because less robust packaging of fertilizing sperm enables greater mobility than in later diverging moths.

evolutionary biology↗

bioRxiv2025

Evolution of highly repetitive silk genes in the Luna moth, Actias luna

Gene duplications are a major driver of molecular diversification and phenotypic evolution. Arthropod silk genes provide an excellent model for studying these processes due to their highly repetitive sequences and rapid evolutionary rates. In Lepidoptera, the Fibroin heavy chain (fibH) gene encodes the primary structural protein for silk fibers, contributing largely to their mechanical strength. This inner fibroin core is surrounded by an outer coating composed primarily of sericins. Sericins are a group of highly repetitive, serine-rich proteins that modulate silk fiber properties. Although sericins in the Domesticated silkworm (Bombyx mori) have been associated with life stage-specific variation in silk characteristics, their evolution and function across Lepidoptera remain poorly understood. Here, we provide a detailed molecular characterization of sericin genes in the Luna moth (Actias luna), a saturniid species known for forming dense, robust, silk-woven cocoons. We identified eight sericin genes that (1) are frequently arranged into clusters of closely related paralogs, (2) exhibit considerable variation in repeat number and amino acid composition, and (3) display distinct gene expression patterns across life stages. A comparison of sericin genes across Saturniidae and Bombycidae reveals evidence for convergent subfunctionalization. These findings suggest that sericin gene duplications enable dynamic shifts in silk composition both within and between species, potentially reflecting adaptive responses to ecological and functional demands. Significance StatementGene duplications are thought to be a major driver of molecular diversification and phenotypic evolution. Arthropod silk genes, characterized by their repetitive sequences and rapid evolution, provide an ideal model for studying these processes. Sericins, a group of highly repetitive, serine-rich silk proteins, are hypothesized to have contributed to the diversification of silk properties, both within and across lepidopteran species. However, their diversity and evolution is poorly understood. Focusing on the Luna moth (Actias luna), we show that sericin gene duplications across Saturniidae have led to subfunctionalization, enabling changes to silk composition. These modifications may represent adaptative responses to ecological and functional demands.

evolutionary biology↗

bioRxiv2025

Genome report: Genome sequence of the hibiscus mealybug, Nipaecoccus viridis (Newstead), an invasive pest of citrus

Mealybugs are frequently known for being pest insects to both ornamental and large-scale agricultural crops. Yet despite their agricultural importance, the genomic resources for this group remain quite small. One such species is the hibiscus mealybug, Nipaecoccus viridis (Newstead) (Hemiptera: Coccomorpha: Pseudococcidae). This invasive mealybug species has recently expanded throughout Florida and has spread across the state. Genomic resources would provide a new means to better understand the invasive nature of this insect, and thus, we present the de novo genome assembly for Nipaecoccus viridis. Our genome assembly is 289 Mb, in which 91.2% of this sequence assembled into 5 chromosomal scaffolds. We report 15,370 genes to be present within our genome. We found that repetitive elements in the genome accounted for 32.40% of the sequence. These statistics follow similar trends to other previously sequenced pseudococcid species.

genomics↗

bioRxiv2025

Gene family evolution reveals dietary adaptations in butterflies and moths

Butterflies and moths (Lepidoptera) are a hyperdiverse lineage of nearly 160,000 described species and their evolutionary success is postulated to be tightly correlated with the radiation of their primary host -- angiosperms. Previous studies found that a significant number of emergent gene families are specific to Lepidoptera, with many genes linked to odorant receptors and peptidases, suggesting that such genetic innovations may be linked to their diversification. Here, we use genomic resources to identify lineage-specific gene families in four nested lepidopteran clades (e.g. Lepidoptera, Glossata, Ditrysia, and Apoditrysia). Among nearly a hundred gene families specific to each group, a handful of gene families have specific and interpretable functions. We found that many digestion-related gene families emerged early in the evolution of Lepidoptera, followed by genes associated with detoxification and immunity. This result aligns with the evolutionary transition in ancient Lepidoptera diets to terrestrial plants, highlighting the emergence of detoxification mechanisms in the megadiverse Ditrysia as a critical adaptation driven by the proliferation of plant chemical defenses. We also found gene families originating from horizontal gene transfer (HGT) events, likely introduced from bacteria and fungi to the common ancestors of Lepidoptera and Ditrysia, respectively. These HGT-derived genes likely played a pivotal role in supporting the dietary transition from algae, diatoms, and aquatic plant debris to fungi and primitive terrestrial plants, ultimately enabling the adaptation to the most dominant angiosperm species.

evolutionary biology↗

bioRxiv2024

Genome report: Genome sequence of the tuliptree scale insect, Toumeyella liriodendri (Gmelin)

Scale insects are of interest both to basic researchers for their unique reproductive biology and to applied researchers for their pest status. In spite of this interest, there remain few genomic resources for this group of insects. To begin addressing this lack of data, we present the genome sequence of the tuliptree scale insect, Toumeyella liriodendri (Gmelin) (Hemiptera: Coccomorpha: Coccidae). The genome assembly spans 536Mb, with over 96% of sequence assembled into one of 17 chromosomal scaffolds. We characterize roughly 66% of this sequence as repetitive and annotate 16,508 protein coding genes. Then we use the reference genome to explore the phylogeny of soft scales (Coccidae) and evolution of karyotype within the family. We find that T. liriodendri is an early-diverging soft scale, less closely related to most sequenced soft scales than a species of the family Aclerdidae is. This molecular result bolsters a previous, character-based phylogenetic placement of Aclerdidae within Coccidae. In terms of genome structure, T. liriodendri has nearly twice as many chromosomes as the only other soft scale assembled to the chromosome level, Ericerus pela (Chavannes). In comparing the two, we find that chromosome number evolution can largely be explained by simple fissions rather than more complex rearrangements. These genomic natural history observations lay a foundation for further exploration of this unique group of insects.

genomics↗

bioRxiv2022

Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes

Insect silk is an incredibly versatile biomaterial. Lepidoptera and their sister lineage, Trichoptera, display some of the most diverse uses of silk with varying strength, adhesive qualities and elastic properties. It is well known that silk fibroin genes are long (> 20 kb) and have many repetitive motifs. These features make these genes challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (Plodia interpunctella) and genomic sequences for the caddisfly, Eubasilissa regina. Both genomes were highly contiguous (N50 = 9.7 Mbp/32.4 Mbp, L50 = 13/11) and complete (BUSCO Complete = 99.3%/95.2%), with complete and contiguous recovery of silk heavy fibroin gene sequences. This study demonstrates that HiFi long-read sequencing can significantly help our understanding of genes with highly contiguous, repetitive regions.

genomics↗

bioRxiv2022

Evolution and diversification dynamics of butterflies

Butterflies are a diverse and charismatic insect group that are thought to have diversified via coevolution with plants and in response to dispersals following key geological events. These hypotheses have been poorly tested at the macroevolutionary scale because a comprehensive phylogenetic framework and datasets on global distributions and larval hosts of butterflies are lacking. We sequenced 391 genes from nearly 2,000 butterfly species to construct a new, phylogenomic tree of butterflies representing 92% of all genera and aggregated global distribution records and larval host datasets. We found that butterflies likely originated in what is now the Americas, [~]100 Ma, shortly before the Cretaceous Thermal Maximum, then crossed Beringia and diversified in the Paleotropics. The ancestor of modern butterflies likely fed on Fabaceae, and most extant families were present before the K/Pg extinction. The majority of butterfly dispersals occurred from the tropics (especially the Neotropics) to temperate zones, largely supporting a "cradle" pattern of diversification. Surprisingly, host breadth changes and shifts to novel host plants had only modest impacts.

evolutionary biology↗

bioRxiv2021

An inexpensive setup for robust activity tracking in small animals: Portable Locomotion Activity Monitor (pLAM)

O_LIAdvances in computer vision and deep learning have automated animal behaviour studies that previously required tedious manual input. However, tracking activity of small and fast flying animals remains a hurdle, especially in a field setting with variable light conditions. Commercial locomotor activity monitors (LAMs) can be expensive, closed source, and generally limited to laboratory settings. C_LIO_LIHere, we present a portable locomotion activity monitor (pLAM), a mobile activity detector to quantify small animal circadian activity. Our setup uses inexpensive components, is based on open-source motion tracking software, and is easy to assemble and use in the field. It runs off-grid, supports low-light tracking with infrared lights, and can implement arbitrary light cycle colours and brightnesses with programmable LEDs. We provide a user-friendly guide to assembling pLAM hardware and accessing its pre-configured software and guidelines for using it in other systems. C_LIO_LIWe benchmarked pLAM for insects under various lab and field conditions, then compared results to a commercial activity detector. They offer broadly similar activity measures, but our setup captures flight and bouts of motion that are often missed by beam-breaking activity detection. C_LIO_LIpLAM will enable high-throughput quantification of small animal location and activity in a low-cost and accessible manner, crucial to studying behaviour that can help inform conservation and management decisions. C_LI

animal behavior and cognition↗