Biology subjects

Markee, A.

Publications and source records attributed to Markee, A..

3 recordsLinked to original sources

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↗