Biology subjects

Kellogg, E.

Publications and source records attributed to Kellogg, E..

6 recordsLinked to original sources

bioRxiv2025

Specialized parallel pathways for adaptive control of visual object pursuit

To pursue a moving visual object, the brain must generate motor commands that continuously steer the object to the center of the visual field via feedback. The gain of this control loop is flexible, yet the biological mechanisms underlying such adaptive control are not well-understood. Here we show that adaptive control in the Drosophila pursuit system involves two parallel pathways. One detects objects in the periphery and steers them toward the center of the visual field. The other detects objects near the center of the visual field and steers them to the visual midline. This latter pathway is flexible: gain increases when the object is moving away from the midline and when the pursuer is running fast. This latter pathway is also preferentially recruited when the fly is aroused, and suppressing it decreases pursuit performance. Our findings demonstrate how adaptive control can emerge from parallel pathways with specialized properties.

neuroscience↗

bioRxiv2025

Extensive genome evolution distinguishes maize within a stable tribe of grasses

Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy - a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives Zea and Tripsacum. In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus Zea, 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.

evolutionary biology↗

bioRxiv2023

Fishing for a reelGene: evaluating gene models with evolution and machine learning

Assembled genomes and their associated annotations have transformed our study of gene function. However, each new assembly generates new gene models. Inconsistencies between annotations likely arise from biological and technical causes, including pseudogene misclassification, transposon activity, and intron retention from sequencing of unspliced transcripts. To evaluate gene model predictions, we developed reelGene, a pipeline of machine learning models focused on (1) transcription boundaries, (2) mRNA integrity, and (3) protein structure. The first two models leverage sequence characteristics and evolutionary conservation across related taxa to learn the grammar of conserved transcription boundaries and mRNA sequences, while the third uses conserved evolutionary grammar of protein sequences to predict whether a gene can produce a protein. Evaluating 1.8 million gene models in maize, reelGene found that 28% were incorrectly annotated or nonfunctional. By leveraging a large cohort of related species and through learning the conserved grammar of proteins, reelGene provides a tool for both evaluating gene model accuracy and genome biology.

genomics↗

bioRxiv2022

Transforming a head direction signal into a goal-oriented steering command

To navigate, we must continuously estimate the direction we are headed in, and we must use this information to guide our path toward our goal1. Direction estimation is accomplished by ring attractor networks in the head direction system2,3. However, we do not understand how the sense of direction is used to guide action. Drosophila connectome analyses4,5 recently revealed two cell types (PFL2 and PFL3) that connect the head direction system to the locomotor system. Here we show how both cell types combine an allocentric head direction signal with an internal goal signal to produce an egocentric motor drive. We recorded their activity as flies navigated in a virtual reality environment toward a goal stored in memory. Strikingly, PFL2 and PFL3 populations are both modulated by deviation from the goal direction, but with opposite signs. The amplitude of PFL2 activity is highest when the fly is oriented away from its goal; activating these cells destabilizes the current orientation and drives turning. By contrast, total PFL3 activity is highest around the goal; these cells generate directional turning to correct small deviations from the goal. Our data support a model where the goal is stored as a sinusoidal pattern whose phase represents direction, and whose amplitude represents salience. Variations in goal amplitude can explain transitions between goal-oriented navigation and exploration. Together, these results show how the sense of direction is used for feedback control of locomotion.

neuroscience↗

bioRxiv2022

Plant conservation assessment at scale: rapid triage of extinction risks

SummaryO_LIThe IUCN Red List criteria are widely used to determine extinction risks of plant and animal life. Here, we use The Red Lists criterion B, Geographic Range Size, to provide preliminary conservation assessments of the members of a large tribe of grasses, the Andropogoneae, with [~]1100 species, including maize, sorghum, and sugarcane and their wild relatives. C_LIO_LIWe use georeferenced occurrence data from the Botanical Information and Ecology Network (BIEN) and automated individual species assessments using ConR to demonstrate efficacy and accuracy in using time-saving tools for conservation research. We validate our results with those from the IUCN-authorized assessment tool, GeoCAT. C_LIO_LIWe discovered a remarkably large gap in digitized information, with slightly more than 50% of the Andropogoneae lacking sufficient information for assessment. ConR and GeoCAT largely agree on which taxa are of least concern (>90%) or possibly threatened (<10%), highlighting that automating assessments with ConR is a viable strategy for preliminary conservation assessments of large plant groups. Results for crop wild relatives are similar to those for the entire data set. C_LIO_LIIncreasing digitization and collection needs to be a high priority. Available rapid assessment tools can then be used to identify species that warrant more comprehensive investigation. C_LI Societal Impact StatementThe current rate of global biodiversity loss creates a pressing need to increase efficiency and throughput of extinction risk assessments in plants. We must assess as many plant species as possible, working with imperfect knowledge, to address the habitat loss and seemingly countless extinction threats of the Anthropocene. Large-scale, preliminary conservation assessments can play a fundamental role in setting priorities for more in-depth investigation.

plant biology↗

bioRxiv2022

A happy accident: a novel turfgrass reference genome

Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled due to the genomes relatively large size and biological complexity that includes apomixis, polyploidy, and interspecific hybridization. We report here a fortuitous de novo assembly and annotation of a P. pratensis genome. Instead of sequencing the genome of a C4 grass, we accidentally sampled and sequenced tissue from a weedy P. pratensis whose stolon was intertwined with that of the C4 grass. The draft assembly consists of 6.09 Gbp with an N50 scaffold length of 65.1 Mbp, and a total of 118 scaffolds, generated using PacBio long reads and Bionano optical map technology. We annotated 256K gene models and found 58% of the genome to be composed of transposable elements. To demonstrate the applicability of the reference genome, we evaluated population structure and estimated genetic diversity in P. pratensis collected from three North American prairies, two in Manitoba, Canada and one in Colorado, USA. Our results support previous studies that found high genetic diversity and population structure within the species. The reference genome and annotation will be an important resource for turfgrass breeding and study of bluegrasses.

plant biology↗