Biology subjects

Levi, T.

Publications and source records attributed to Levi, T..

18 recordsLinked to original sources

bioRxiv2026

Symbolic regression for empirically realistic population dynamic time series

Applications of machine learning in ecology are rapidly expanding. Symbolic regression is gaining particular attention for its success in reverse-engineering human-readable explanatory population models, including the logistic growth and Lotka-Volterra equations, from simulated and laboratory-based population time series. However, field-based populations often lack the characteristics of the idealized time series used in prior assessments. We evaluated the utility of symbolic regression for such time series by quantifying its success for synthetic data varying in sampling density, population cycle asymmetry, process noise, and the erroneous consideration of spurious variables. We further compared two data preprocessing options for estimating population growth rates, and four evaluation workflows for selecting equations. Results indicate that a trade-off between sampling density and process noise primarily drives equation and variable recovery. Symbolic regression failed to recover the underlying equation at sampling densities below 10 points per cycle; however, at higher sampling densities, process noise did increase equation recovery rates. Importantly, although the true model was frequently recovered at sampling densities of 25 or more points per cycle, it was not consistently selected by the evaluation workflows. This discrepancy highlights a need for more robust post-algorithm selection criteria to identify the focal equation among competing candidates.

ecology↗

bioRxiv2025

The effects of predator recovery and climate change on the long-term demography of a flagship herbivore

In the western United States, ecosystems are being reshaped from both bottom-up and top-down processes. Widespread carnivore recolonizations after 20th century extirpations have returned top-down pressures to ecosystems, and climate change is reshaping bottom-up forces through shifts in the timing and length of growing seasons, resulting in reduced forage quality and quantity. Large herbivores, such as elk (Cervus canadensis), function as flagship species for conservation and have potential for both top-down and bottom-up forces to shape demography as ecosystems change. To test the roles of top-down (puma density (Puma concolor)) and bottom-up (drought severity and elk density) processes in shaping large herbivore demography, and to tie those effects to population trajectories, we built an integrated population model (IPM) using 36 years of elk data spanning the recolonization of pumas and long-term climate change in eastern Oregon, USA. We tested the effects of top-down and bottom-up forces on elk recruitment, calf survival, and population growth. We also tested effects of bottom-up forces on elk pregnancy rates. Puma recolonization corresponded with declines in mean recruitment from 0.44 to 0.32 calves per female and in calf survival from 0.92 to 0.69, corresponding with a 4% drop in population growth. Drought severity increased over our study period, explaining a decline in mean recruitment from 0.39 to 0.32 calves per female, which corresponds to a 3% reduction in population growth. Drought severity likely acted on recruitment through reduced pregnancy rates. Lactating females showed lower pregnancy rates in drought conditions, while drought from fall breeding periods to the following fall had no effect on recruitment. While both top-down and bottom-up forces explained variation in elk demography over the course of our study, bottom-up forces are likely to be more influential on large herbivores moving forward. Predator populations stabilized following recovery, limiting the top-down contribution to annual variation in vital rates. Climate change-induced drought patterns, however, are accelerating during summer and fall throughout large areas of the interior western U.S. Thus, our results indicate the potential for increasingly strong bottom-up negative effects on herbivores whose performance depends on a narrow period of summer nutrition. Open Research StatementData are not yet provided. Many of the data from Starkey Experimental Forest and Range are already publicly available, and we are currently working to post data for this manuscript on the Forest Service Research Data Archive (FSRDA) linked to the rest of the data from Starkey. Upon acceptance, all data and the relevant code will be archived the FSRDA. Currently, the code for the paper is publicly available on Github at https://github.com/keloonam/starkey_ipm

ecology↗

bioRxiv2024

Variability and correlations among vital rates and their influence on population growth in mule and black-tailed deer

To reverse observed range-wide population declines, managers of mule and black- tailed deer (Odocoileus hemionus) require information on the vital rates and life stages that are most influential to population growth for which to target management actions. We conducted a range-wide literature review and used hierarchical models to provide biological descriptions of mule and black-tailed deer vital rates, their variability, and how they correlate with one another. We then used matrix models and life-stage simulation analysis to determine the individual vital rates that contributed most to lambda, i.e., annual population growth rate. Adult female survival was the vital rate with the greatest ability to predict lambda and explained 62% of the variation in population growth. While annual juvenile survival explained 44% of the variation in lambda, summer and winter juvenile survival by themselves were far less explanatory than adult female survival. Winter fawn:doe ratios, a metric often collected by management agencies, only explained 10% of the variation in lambda. When adult female survival was 0.84, our simulations estimated an equal probability that a population would increase versus decrease, and correspondingly, the estimate of lambda was 1.0 with a 95% credible interval of 0.88-1.14. Simulations suggested that populations with adult survival rates less than 70% would always decline, but as survival increased beyond this value lambda increased linearly and never plateaued. In contrast, the probability of observing a stable lambda plateaued when annual juvenile survival reached approximately 0.5. The mean lambda calculated from all simulated values within the observed range of vital rate values across the species geographical distribution was 0.975, and in 61% of the simulations lambda was < 1. After 20 years, we estimated that this distribution of lambda values would cause populations to decrease in 92% of instances with a mean decrease of 44%. Our results align with the observed declines in mule deer populations throughout their range over recent decades and suggest that these trends will continue until management can improve survival of adult females.

ecology↗

bioRxiv2023

Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity

Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into many-row (observation), many-column (species) datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These novel community datasets let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers within a joint species distribution model. With this approach, we generate distribution maps for 76 arthro-pod species across a 225 km2 temperate-zone forested landscape. We combine the maps to visualise the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this sideways biodiversity modelling method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres.

ecology↗

bioRxiv2023

BioemuS: A new tool for neurological disorders studies through real-time emulation and hybridization using biomimetic SpikingNeural Network

Characterization and modeling of biological neural networks has emerged as a field driving significant advancements in our understanding of brain function and related pathologies. As of today, pharmacological treatments for neurological disorders remain limited, pushing the exploration of promising alternative approaches such as electroceutics. Recent research in bioelectronics and neuromorphic engineering have led to the design of the new generation of neuroprostheses for brain repair. However, its complete development requires deeper understanding and expertise in biohybrid interaction. Here, we show a novel real-time, biomimetic, cost-effective and user-friendly neural network for bio-hybrid experiments and real-time emulation. Our system allows investigation and reproduction of biophysically detailed neural network dynamics while promoting cost-efficiency, flexibility and ease of use. We showcase the feasibility of conducting biohybrid experiments using standard biophysical interfaces and various biological cells as well as real-time emulation of complex models. We anticipate our system to be a step towards developing neuromorphicbased neuroprostheses for bioelectrical therapeutics by enabling communication with biological networks on a similar time scale, facilitated by an easy-to-use and accessible embedded real-time system. Our real-time device further enhances its potential for practical applications in biohybrid experiments.

neuroscience↗

bioRxiv2022

Neural coding of temperature with a DNA-based spiking chemical neuron

Complex organisms perceive their surroundings with sensory neurons which encode physical stimuli into spikes of electrical activities. The past decade has seen reports of DNA-based chemical neurons that mimic artificial neural networks with chemical reactions. Yet, they lack the physical sensing and temporal coding of sensory biological neurons. Here we report a thermosensory chemical neuron based on DNA and enzymes that spikes with chemical activity when exposed to cold. Surprisingly, this chemical neuron shares deep mathematical similarities with a toy model of a cold nociceptive neuron: they follow a similar bifurcation route between rest and oscillations and avoid artefacts associated with canonical bifurcations (such as irreversibility, damping or untimely spiking). We experimentally demonstrate this robustness by encoding - digitally and analogically - thermal messages into chemical waveforms. This chemical neuron could pave the way for implementing in DNA the third generation of neural network models (spiking networks), and opens the door for associative learning. One-Sentence SummaryA DNA-based chemical network mathematically mimics the sensing of cold by a biological neuron.

biochemistry↗

bioRxiv2022

Western spotted skunks provide important food web linkages in forest of the Pacific Northwest

There are increasing concerns about the decreasing population trends of small mammalian carnivores around the world. With limited knowledge about their ecology and natural history, small mammal conservation and management remains difficult. To address one of these deficiencies for western spotted skunks (Spilogale gracilis), we investigated their diet in the Oregon Cascades of the Pacific Northwest during 2017 - 2019. We collected 130 spotted skunk scats opportunistically and with detection dog teams and identified prey items using DNA metabarcoding and mechanical sorting. Western spotted skunk diet consisted of invertebrates such as wasps, millipedes, and gastropods, vertebrates such as small mammals, amphibians, and birds, and plants such as Gaultheria, Rubus, and Vaccinium. Diet also consisted of items such as black-tailed deer that were likely scavenged. Comparison in diet by season revealed that spotted skunks consumed more insects during the dry season (June - August) and marginally more mammals during the wet season (September - May). We observed similar diet in areas with no record of human disturbance and areas with a history of logging. Western spotted skunks provide important food web linkages between aquatic, terrestrial, and arboreal systems by facilitating energy and nutrient transfer, and serve important functional roles of seed dispersal and scavenging. Through prey-switching, western spotted skunks may dampen the effects of irruptions of prey, such as wasps during dry springs and summers, which could then provide ecosystem resilience to environmental change.

ecology↗

bioRxiv2021

A seasonal pulse of ungulate neonates influences space use by carnivores in a multi-predator, multi-prey system

O_LIThe behavioral mechanisms by which predators encounter prey are poorly resolved. In particular, the extent to which predators engage in active search for prey versus incidentally encountering them is unknown. The distinction between search and incidental encounter influences prey population dynamics with active search exerting a stabilizing force on prey populations by alleviating predation pressure on low-density prey and increasing it for high-density prey. C_LIO_LIParturition of many large herbivores occurs during a short and predictable temporal window in which young are highly vulnerable to predation. Our study aims to determine how a suite of carnivores responds to the seasonal pulse of newborn ungulates using contemporaneous GPS locations of four species of predators and two species of prey. C_LIO_LIWe used step-selection functions to assess whether coyotes, cougars, black bears, and bobcats actively searched for parturient females in a low-density population of mule deer and a high-density population of elk. We then assessed whether searching carnivores shifted their habitat use toward areas exhibiting a high probability of encountering neonates. C_LIO_LINone of the four carnivore species encountered parturient mule deer more often than expected by chance suggesting that predation of young resulted from incidental encounters. By contrast, we determined that cougar and male bear movements positioned them in proximity of parturient elk more often than expected by chance which is evidence of searching behavior. Although both male bears and cougars searched for neonates, only male bears used elk parturition habitat in a way that dynamically tracked the phenology of the elk birth pulse suggesting that maximizing encounters with juvenile elk was a motivation when selecting resources. C_LIO_LIOur results support the existence of a stabilizing mechanism to prey populations through active search behavior by predators because carnivores in our study searched for the high-density prey species (elk) but ignored the low-density species (mule deer). We conclude that prey density must be high enough to warrant active search, and that there is high interspecific and intersexual variability in foraging strategies among large mammalian predators and their prey. C_LI

ecology↗

bioRxiv2021

Nucleoporin107 mediates female sexual differentiation via Dsx

We recently identified a missense mutation in Nucleoporin107 (Nup107; D447N) underlying XX-ovarian-dysgenesis, a rare disorder characterized by underdeveloped and dysfunctional ovaries. Modelling of the human mutation in Drosophila or specific knockdown of Nup107 in the gonadal soma resulted in ovarian-dysgenesis-like phenotypes. Transcriptomic analysis identified the somatic sex-determination gene doublesex (dsx) as a target of Nup107. Establishing Dsx as a primary relevant target of Nup107, either loss or gain of Dsx in the gonadal soma is sufficient to mimic or rescue the phenotypes induced by Nup107 loss. Importantly, the aberrant phenotypes induced by compromising either Nup107 or dsx are reminiscent of BMP signaling hyperactivation. Remarkably, in this context, the metalloprotease AdamTS-A, a transcriptional target of both Dsx and Nup107, is necessary for the calibration of BMP signaling. As modulation of BMP signaling is a conserved critical determinant of soma-germline interaction, the sex and tissue specific deployment of Dsx-F by Nup107 seems crucial for the maintenance of the homeostatic balance between the germ cells and somatic gonadal cells.

developmental biology↗

bioRxiv2021

Extensive aquatic subsidies lead to territorial breakdown and high density of an apex predator

Energetic subsidies between terrestrial and aquatic ecosystems can strongly influence food webs and population dynamics. Our objective was to study how aquatic subsidies affected jaguar (Panthera onca) diet, sociality, and population density in a seasonally flooded protected area in the Brazilian Pantanal. The diet (n = 138 scats) was dominated by fish (46%) and aquatic reptiles (55%), representing the first jaguar population known to feed extensively on fish and to minimally consume mammals (11%). These aquatic subsidies supported the highest jaguar population density estimate to date (12.4 per 100 km2) derived from camera traps (8,065 trap nights) and GPS collars (n = 13). Contrary to their mostly solitary behavior elsewhere, we documented social interactions previously unobserved between same-sex adults including cooperative fishing, co-traveling, and play. Our research demonstrates that aquatic subsidies seen in omnivores can be highly influential to obligate carnivores leading to high population density and altered social structure.

ecology↗

bioRxiv2021

Predicted distribution of a rare and understudied forest carnivore: Humboldt martens (Martes caurina humboldtensis)

BackgroundA suite of mammalian species have experienced range contractions following European settlement and post-settlement development of the North American continent. For example, while North American martens (American marten, Martes americana; Pacific marten, M. caurina) generally have a broad range across northern latitudes, local populations have experienced substantial reductions in distribution and some extant populations are small and geographically isolated. The Humboldt marten (M. c. humboldtensis), a subspecies of Pacific marten that occurs in coastal Oregon and northern California, was recently designated as federally threatened in part due to its reduced distribution. To inform strategic conservation actions, we assessed Humboldt marten occurrence by compiling all known records from their range. MethodsWe compiled Humboldt marten locations since their rediscover to present (1,692 marten locations, 1996-2020). We spatially-thinned locations to 500-m to assess correlations with variables across contemporary Humboldt marten distribution (n=384). Using maximum entropy modeling (Maxent), we created distribution models with variables optimized for spatial scale; pre-selected scales were associated with marten ecology (50 to 1170 m radius). Marten locations were most correlated with abiotic factors (e.g., precipitation), which are unalterable and therefore uninformative within the context of restoration or management actions. Thus, we created variables to focus on hypothesized marten habitat relationships, including understory conditions such as predicted suitability of shrub species. ResultsHumboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon), mast producing trees), increased pine (Pinus sp) overstory cover and precipitation at home-range spatial scales, areas with low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature on the species, we found little evidence that Humboldt marten locations were associated with old growth structural indices, perhaps because of a potential mismatch in the association between this index and shrub cover. As with any species distribution model, there were gaps in predicted distribution where Humboldt martens have been located during more recent surveys, for instance the southeastern portion of Oregons coast range. Conservation efforts and our assessment of potential risks to Humboldt marten populations would benefit from additional information on range extent, population sizes, and fine-scale habitat use. Like many rare and lesser-known species, this case study provides an example of how limited information can provide differing interpretations, emphasizing the need for study-level replication in ecology.

ecology↗

bioRxiv2021

Games of risk and reward in carnivore communities

Mesopredator release theory suggests that dominant predators suppress subordinate carnivores and ultimately shape community dynamics, but the assumption that subordinate species are only negatively affected ignores the possibility of facilitation through scavenging. We examined the interplay within a carnivore community consisting of cougars, coyotes, black bears, and bobcats using contemporaneous Global Positioning System telemetry data from 51 individuals, diet analysis from 972 DNA-metabarcoded scats, and data from 128 physical investigations of cougar kill sites, 28 of which were monitored with remote cameras. Resource provisioning from competitively-dominant cougars to coyotes through scavenging was so prolific as to be an overwhelming determinant of coyote behavior, space use, and resource acquisition. This was evident via strong attraction of coyotes to cougar kill sites, frequent scavenging of cougar-killed prey, and coyote diets that nearly matched cougars in the magnitude of ungulate consumption. Yet coyotes were often killed by cougars and used space to minimize encounters, complicating the fitness benefits gained from scavenging. We estimated that 23% (95% CI: 8-55%) of the coyote population in our study area was killed by cougars annually suggesting that coyote interactions with cougars are a complex behavioral game of risk and reward. In contrast, we found no indication that bobcat space use or diet was influenced by cougars. Black bears avoided cougars, but there was no evidence of attraction to cougar kill sites, and much lower levels of ungulate consumption and carcass visitation than for coyotes. Interspecific interactions among carnivores are multifaceted encompassing both suppression and facilitation. Significance StatementAn incomplete understanding of the total influence competitively-dominant predators exert on subordinate species hinders our ability to anticipate the effects that changing carnivore populations will have in ecological communities. Here we show that cougars are the architects of a complex behavioral game of risk and reward, as subordinate or co-occurring carnivores are both provisioned and preyed on by the dominant predators. Each co-occurring carnivore species considered here employed a different strategy to approach the risk-reward tradeoff suggesting there are multiple viable solutions to the game. By not considering the multitude of effects dominant predators have on other carnivores, we are missing important linkages in terrestrial food webs.

ecology↗

bioRxiv2020

Integrating spatial capture-recapture models with variable individual identifiability

Spatial capture-recapture (SCR) models have become the preferred tool for estimating densities of carnivores. Within this family of models are variants requiring identification of all individuals in each encounter (SCR), a subset of individuals only (generalized spatial mark-resight, gSMR), or no individual identification (spatial count or spatial presence-absence). Although each technique has been shown through simulation to yield unbiased results, the consistency and relative precision of estimates across methods in real-world settings are seldom considered. We tested a suite of models ranging from those only requiring detections of unmarked individuals to others that integrate remote camera, physical capture, genetic, and global positioning system (GPS) data into a hybrid model, to estimate population densities of black bears, bobcats, cougars, and coyotes. For each species we genotyped fecal DNA collected with detection dogs during a 20-day period. A subset of individuals from each species was affixed with GPS collars bearing unique markings and resighted by remote cameras over 140 days contemporaneous with scat collection. Camera-based gSMR models produced density estimates that differed by less than 10% from genetic SCR for bears, cougars, and coyotes once important sources of variation (sex or behavioral status) were controlled for. For bobcats, SCR estimates were 33% higher than gSMR. The cause of the discrepancies in estimates was likely attributable to challenges designing a study compatible for species with disparate home range sizes and the difficulty of collecting sufficient data in a timeframe in which demographic closure could be assumed. Unmarked models estimated densities that varied greatly from SCR, but estimates became more consistent in models wherein more individuals were identifiable. Hybrid models containing all data sources exhibited the most precise estimates for all species. For studies in which only sparse data can be obtained and the strictest model assumptions are unlikely to be met, we suggest researchers use caution making inference from models lacking individual identity. For best results, we further recommend the use of methods requiring at least a subset of the population is marked and that multiple datasets are incorporated when possible.

ecology↗

bioRxiv2019

Comparison of mechanical sorting and DNA metabarcoding for diet analysis with degraded wolf scats

DNA metabarcoding has become a powerful technique for identifying species and profiling biodiversity with the potential to improve efficiency, reveal rare prey species, and correct mistaken identification error in diet studies. However, the extent to which molecular approaches agree with traditional approaches is unknown for many species. Here, we compare diets from wolf scats profiled using both mechanical sorting and metabarcoding of amplified vertebrate DNA sequences. Our objectives were: (1) compare findings from mechanical sorting and metabarcoding as a method of diet profiling and (2) use results to better understand diets of wolves on Prince of Wales Island, a population of conservation concern. We predicted metabarcoding would reveal both higher diversity of prey and identify rare species that are overlooked with mechanical sorting. We also posited that the relative contribution of Sitka black-tailed deer (Odocoileus hemionus sitkensis) and beaver (Castor canadensis) would be overestimated with mechanical sorting methods because of the failure to account for the full diet diversity of these wolves. We found that there was substantial overlap in the diets revealed using both methods, indicating that deer, beaver, and black bear (Ursus americanus) were the primary prey species. However, there was a large discrepancy in the occurrence of beaver in scats (54% and 24% from mechanical sorting and metabarcoding, respectively) explained by the high rate of false positives with mechanical sorting methods. Metabarcoding revealed more diet diversity than mechanical sorting, thus supporting our initial predictions. Prince of Wales Island wolves appear to have a more diverse diet with greater occurrence of rare species than previously described including 14 prey species that contribute to wolf diet. Metabarcoding is an effective method for profiling carnivore diet and enhances our knowledge concerning the full diversity of wolf diets, even in the extremely wet conditions of southeast Alaska, which can lead to DNA degradation. Given the increasingly efficient and cost-effective nature of collecting eDNA, we recommend incorporating these molecular methods into field-based projects to further examine questions related to increased use of alternate prey coinciding with changes in abundance of primary prey and habitat alteration.

ecology↗

bioRxiv2019

More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing

Non-invasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates, and high error rates. The information lost when genotyping success is low may lead to decreased precision in animal population densities which could misguide conservation and management actions. Single nucleotide polymorphisms (SNPs) provide a promising alternative to traditionally used microsatellites as SNPs allow amplification of shorter DNA fragments, are less prone to genotyping errors, and produce results that are easily shared among laboratories. Here, we outline a detailed protocol for cost-effective and accurate noninvasive SNP genotyping using highly multiplexed amplicon sequencing optimized for degraded DNA. We validated this method for individual identification by genotyping 216 scats, 18 hairs and 15 tissues from coyotes (Canis latrans). Our genotyping success rate for scat samples was 93%, and 100% for hair and tissue, representing a substantial increase compared to previous microsatellite-based studies at a cost of under $5 per PCR replicate (excluding labor). The accuracy of the genotypes was further corroborated in that genotypes from scats matching known, GPS-collared coyotes were always located within the territory of the known individual. We also show that different levels of multiplexing produced similar results, but that PCR product cleanup strategies can have substantial effects on genotyping success. By making noninvasive genotyping more affordable, accurate, and efficient, this research may allow for a substantial increase in the use of noninvasive methods to monitor and conserve free-ranging wildlife populations.

ecology↗

bioRxiv2019

Environmental DNA for indigenous-led monitoring of a culturally important fish

Although environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends rather than simply assessing presence or absence. However, the efficacy of environmental-DNA-based indices of abundance for long-term population monitoring have not yet been assessed. Here we report on the relationship between six years of mark-recapture population estimates for eulachon (Thaleichthys pacificus) and eDNA rates, which are calculated from the product of stream flow and DNA concentration. Eulachon are a culturally and biologically important anadromous fish that have significantly declined in the southern part of their range but were historically rendered into oil and traded. Both the peak eDNA rate and the area under the curve of the daily eDNA rate were highly predictive of the mark-recapture population estimate, explaining 84.96% and 92.53% of the deviance respectively. Even in the absence of flow correction, the peak of the daily eDNA concentration explained an astonishing 89.53% while the area under the curve explained 90.74% of the deviance. These results support the use of eDNA to monitor eulachon population trends and represent a >80% cost savings over mark-recapture, which could be further increased with automated water sampling, reduced replication, and focused temporal sampling. Due to its logistical ease and affordability, eDNA sampling can facilitate monitoring a larger number of rivers and in remote locations where mark-recapture is infeasible.

ecology↗

bioRxiv2019

A neuroprosthetic system to restore neuronal communication in modular networks

Recent advances in neurotechnology allow neurological impairments to be treated or reduced by brain machine interfaces and neuroprostheses. To develop energy-efficient and real-time capable devices, neuromorphic computing systems are envisaged as the core of next-generation neurobiohybrid systems for brain repair. We demonstrate here the first exploitation of a neuromorphic prosthesis to restore bidirectional interactions between two neuronal populations, even when one is damaged or completely missing. We used in vitro modular cell cultures to mimic the mutual interaction between neuronal assemblies and created a focal lesion to functionally disconnect the two populations. Then, we employed our neuromorphic prosthesis for two specific applications with future clinical implications: bidirectional bridging to artificially reconnect two disconnected neuronal modules and hybrid bidirectional bridging to replace the activity of one module with a neuromorphic spiking neural network. Our neuroprosthetic system opens up new avenues for the development of novel bioelectrical therapeutics for human applications.

bioengineering↗

bioRxiv2018

Environmental DNA for the enumeration and management of Pacific salmon

Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over [~]US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar. The ability to detect organisms by shed tissue (environmental DNA, eDNA) promises a more efficient counting method. However, although eDNA correlates generally with local fish abundances, we do not know if eDNA can accurately enumerate salmon. Here we show that daily, and near-daily, flow-corrected eDNA rate closely tracks daily numbers of returning sockeye and coho spawners and outmigrating sockeye smolts. eDNA thus promises accurate and efficient enumeration, but to deliver the most robust numbers will need higher-resolution stream-flow data, at-least-daily sampling, and a focus on species with simple life histories, since shedding rate varies amongst jacks, juveniles, and adults.

ecology↗