Biology subjects

Wilson, M. L.

Publications and source records attributed to Wilson, M. L..

13 recordsLinked to original sources

bioRxiv2026

Ranging and territoriality in African Apes

Intergroup relations vary strikingly among African apes, with only chimpanzees showing intense, often lethal territoriality. The economic defendability hypothesis proposes that such territorial behaviour is favored where home ranges can be economically defended, as indexed by the ratio of daily travel distance to home range diameter. To test this idea, we compiled and analyzed comparable data on yearly home range size, daily travel distance and defendability indices from one population of each nonhuman African ape species and integrated these with comparable published data. We find that bonobos had substantially larger home ranges and longer daily travel distances than chimpanzees and gorillas, contradicting a prevailing assumption that bonobos experience higher or more reliable food abundance. Defendability indices were higher in chimpanzees and bonobos than in mountain gorillas, but did not differ significantly between chimpanzees, bonobos, and western gorillas. Overall, our results indicate that economic defendability alone cannot explain interspecific variation in territoriality and that our current understanding of ecological differences between the species of the genus Pan have to be revised. Possible additional factors shaping space use of neighboring groups include mate competition within groups.

animal behavior and cognition↗

bioRxiv2025

Origin, domestication, and diversity of the climate resilient Ethiopian cereal teff

Teff (Eragrostis tef) is a climate-resilient cereal and staple crop in the Horn of Africa, cultivated by millions of smallholder farmers. Despite its cultural and nutritional significance, teff has limited genomic tools, constraining progress in yield improvement and trait optimization. Here, we assembled and resequenced the Teff Association Panel (TAP), a diverse set of 265 landraces and cultivars, to investigate the domestication history, genetic diversity, and agronomic traits of teff. Phylogenetic and population genetic analyses confirm Eragrostis pilosa as the direct progenitor of teff, with domestication likely occurring in the Tigray region of Ethiopia. We generated a high-quality reference genome for E. pilosa and found extensive chromosomal collinearity and minimal gene loss compared to teff, with teff-specific genes enriched in functions related to domestication traits. We identified signatures of selection across the teff genome and used genome-wide association studies (GWAS) to map loci associated with seed color and panicle architecture. Integrated GWAS, expression, metabolic, and comparative genomic analyses pinpoint a major seed color locus containing orthologs of the TT7 cytochrome P450 gene involved in flavonoid hydroxylation and the TT2 MYB transcription factor regulating proanthocyanidin biosynthesis. For panicle architecture, we identified a strong association near a teff ortholog of Dense and Erect Panicle 1 (DEP1), a key regulator of inflorescence structure in rice and sorghum. This suggests convergent selection on shared genetic pathways controlling panicle morphology across cereals. Our findings confirm the evolutionary origin of teff, identify key domestication loci, and highlight untapped genetic diversity among Ethiopian breeding lines. These genomic resources provide a foundation for accelerating teff improvement through molecular breeding and genome editing to enhance yield, resilience, and nutrition.

plant biology↗

bioRxiv2024

Scaling laws of plasmids across the microbial tree of life

Plasmids play a critical role in shaping the dynamics and evolution of microbial communities. The capacity of a plasmid to express genes is constrained by two parameters: length and copy number. However, the interplay between these parameters and their constraints on plasmid evolution have remained elusive due to the absence of comprehensive quantitative analyses. To address this gap, we developed Probabilistic Iterative Read Assignment (PIRA), a new computational method that overcomes previous computational bottlenecks, enabling rapid and accurate determination of plasmid copy numbers at an unprecedented scale. Applying PIRA to all microbial genomes in the NCBI RefSeq database with linked short-read sequencing data in the Sequencing Read Archive (SRA), we analyzed 4,317 bacterial and archaeal genomes encompassing 11,338 plasmids, spanning the microbial tree of life. Our analysis reveals three scaling laws of plasmids: first, an inverse power-law correlation between plasmid copy number and plasmid length; second, a positive linear correlation between protein-coding genes and plasmid length; and third, a positive correlation between metabolic genes per plasmid and plasmid length, particularly for large plasmids. These scaling laws imply fundamental constraints on plasmid evolution and functional organization, indicating that as plasmids increase in length, they converge toward chromosomal characteristics in copy number and functional content. Our findings not only advance the understanding of plasmid dynamics but also have implications for microbial evolution, biotechnology, and the design of synthetic plasmids. SignificanceBy discovering universal scaling laws and developing a new computational method to compute plasmid copy numbers across the microbial tree of life, we show that as plasmids increase in length, they converge to chromosomes in their copy number and their coding and metabolic properties. This insight reveals fundamental principles governing plasmid evolution and has implications for biotechnology and medicine.

microbiology↗

bioRxiv2024

Variability in drought gene expression datasets highlight the need for community standardization

Physiologically relevant drought stress is difficult to apply consistently, and the heterogeneity in experimental design, growth conditions, and sampling schemes make it challenging to compare water deficit studies in plants. Here, we re-analyzed hundreds of drought gene expression experiments across diverse model and crop species and quantified the variability across studies. We found that drought studies are surprisingly uncomparable, even when accounting for differences in genotype, environment, drought severity, and method of drying. Many studies, including most Arabidopsis work, lack high-quality phenotypic and physiological datasets to accompany gene expression, making it impossible to assess the severity or in some cases the occurrence of water deficit stress events. From these datasets, we developed supervised learning classifiers that can accurately predict if RNA-seq samples have experienced a physiologically relevant drought stress, and suggest this can be used as a quality control for future studies. Together, our analyses highlight the need for more community standardization, and the importance of paired physiology data to quantify stress severity for reproducibility and future data analyses.

plant biology↗

bioRxiv2024

Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component, Mios

Reproductive success relies on proper establishment and maintenance of biological sex. In many animals, including mammals, the primary gonad is initially ovary in character. We previously showed the RNA binding protein (RNAbp), Rbpms2, is required for ovary fate in zebrafish. Here, we identified Rbpms2 targets in oocytes (Rbpms2-bound oocyte RNAs; rboRNAs). We identify Rbpms2 as a translational regulator of rboRNAs, which include testis factors and ribosome biogenesis factors. Further, genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway, specifically through the mTorc1-activating Gap activity towards Rags 2 (Gator2) component, Missing oocyte (Mios). Cumulatively, our findings indicate that early gonocytes are in a dual poised, bipotential state in which Rbpms2 acts as a binary fate-switch. Specifically, Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2-mediated checkpoint, thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis.

developmental biology↗

bioRxiv2023

Programming dynamic division of labor using horizontal gene transfer

The metabolic engineering of microbes has broad applications, including in biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multi-step pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is division of labor (DOL), in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted inter-strain population dynamics. Through modeling, we show that dynamic division of labor (DDOL) mediated by horizontal gene transfer (HGT) can overcome these limitations and enable the robust maintenance of burdensome, multi-step pathways. We also use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.

synthetic biology↗

bioRxiv2021

Effects of anesthesia on ozone-induced lung and systemic inflammation

Anesthetics are required for procedures that deliver drugs/biologics, infectious/inflammatory agents, and toxicants directly to the lungs. However, the possible confounding effects of anesthesia on lung inflammation and injury are underreported. Here, we tested the effects of brief isoflurane (Iso) or ketamine/xylazine/atipamezole (K/X/A) anesthesia prior to ozone exposure (4 hours, 3ppm) on lung inflammatory responses in mice. Anesthesia regimens modeled those used for non-surgical intratracheal instillations, and were administered 1-2 hours or 24 hours prior to initiating ozone exposure. We found that Iso given 1-2 hours prior to ozone inhibited inflammatory responses in the lung, and this effect was absent when Iso was given 23-24 hours prior to ozone. In contrast, K/X/A given 1-2 hours prior to ozone increased lung and systemic inflammation. Our results highlight the need to comprehensively evaluate anesthesia as an experimental variable in the assessment of lung inflammation in response to ozone and other inflammatory stimuli.

physiology↗

bioRxiv2021

Effects of ozone on sickness and depressive-like behavioral and biochemical phenotypes and their relations to serum amyloid A and kynurenine in blood

Ozone (O3) is an air pollutant which primarily damages the lungs, but growing evidence supports that O3 exposure can also affect the brain. Serum amyloid A (SAA) and kynurenine have been identified as circulating factors that are upregulated by O3, and both can contribute to depressive-like behaviors in mice. However, little is known about the relations of O3 exposure to sickness and depressive-like behaviors in experimental settings. In this study, we evaluated O3 dose-, time- and sex-dependent changes in circulating SAA in context of pulmonary inflammation and damage, sickness and depressive-like behavioral changes, and systemic changes in kynurenine and indoleamine 2,3-dioxygenase (IDO), an enzyme that regulates kynurenine production and contributes to inflammation-induced depressive-like behaviors. Our results in Balb/c and CD-1 mice showed that 3ppm O3, but not 2 or 1ppm O3, caused elevations in serum SAA and pulmonary neutrophils, and these responses resolved by 48 hours. Sickness and depressive-like behaviors were observed at all O3 doses (1-3ppm), although the detection of certain behavioral changes varied by dose. We also found that Ido1 mRNA expression was increased in the brain and spleen 24 hours after 3ppm O3, and that kynurenine was increased in blood. Together, these findings indicate that acute O3 exposure induces transient symptoms of sickness and depressive-like behaviors which may occur in the presence or absence of overt pulmonary neutrophilia and systemic increases of SAA. We also present evidence that the IDO/kynurenine pathway is upregulated systemically following an acute exposure to O3 in mice.

physiology↗

bioRxiv2021

Chimpanzee pant-hoots encode information about individual but not group differences

Vocal learning, the ability to voluntarily modify the acoustic structure of vocalizations based on social cues, is a fundamental feature of speech in humans (Homo sapiens). While vocal learning is common in taxa such as songbirds and whales, the vocal learning capacities of nonhuman primates appear more limited. Intriguingly, evidence for vocal learning has been reported in chimpanzees (Pan troglodytes), for example in the form of regional variation ( dialects) in the pant-hoot calls. This suggests that some capacity for vocal learning may be an ancient feature of the Pan-Homo clade. Nonetheless, reported differences have been subtle, with inter-community variation representing only a small portion of the total acoustic variation. To gain further insights into the extent of regional variation in chimpanzee vocalizations, we performed an analysis of pant-hoots from chimpanzees in the neighboring Kasekela and Mitumba communities at Gombe National Park, Tanzania, and the geographically distant Kanyawara community at Kibale National Park, Uganda. We observed group differences only among the geographically isolated communities and did not find any differences between the neighboring communities at Gombe. Furthermore, we found differences among individuals in all communities. Hence, the variation in chimpanzee pant-hoots reflected individual differences, rather than group differences. The limited evidences for vocal learning in Pan suggest that extensive vocal learning emerged in the human lineage after the divergence from Pan.

animal behavior and cognition↗

bioRxiv2020

Playbacks of Food-associated Calls Attract Chimpanzees Towards Known Food Patches in a Captive Setting

Food-associated calls have attracted much research attention due to their potential to refer to discovered food in a word-like manner. Nevertheless, their effect on receiver behavior remains unclear for many species. While some studies suggest that food-associated calls attract other foragers, other studies indicate that they repel others. We conducted playback studies to differentiate between these two hypotheses for the function of the chimpanzee (Pan troglodytes) food-associated rough grunt. We tested how acoustic playbacks of rough grunts (or control calls) from one of two known, identical food patches affected receivers foraging decisions in a captive setting. We found that participants were more likely than chance to first investigate the patch from which rough-grunts, but not control calls, were broadcast. However, neither condition increased the likelihood that participants fed first from a given patch. Our results support the hypothesis that rough-grunts attract receivers. However, since receivers were already aware of the presence of food, our results question whether rough-grunts attract by conveying information about discovered food, or rather, the signalers motivational state.

animal behavior and cognition↗

bioRxiv2020

Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves

Premise of studyLeaf morphology is dynamic, continuously deforming during leaf expansion and among leaves within a shoot. We measured leaf morphology from over 200 vines over four years, and modeled changes in leaf shape along the shoot to determine if a composite "shape of shapes" can better capture variation and predict species identity compared to individual leaves. MethodsUsing homologous universal landmarks found in grapevine leaves, we modeled various morphological features as a polynomial function of leaf node. The resulting functions are used to reconstruct modeled leaf shapes across shoots, generating composite leaves that comprehensively capture the spectrum of possible leaf morphologies. ResultsWe found that composite leaves are better predictors of species identity than individual leaves from the same plant. We were able to use composite leaves to predict species identity of previously unassigned vines, which were verified with genotyping. DiscussionObservations of individual leaf shape fail to capture the true diversity between species. Composite leaf shape--an assemblage of modeled leaf snapshots across the shoot--is a better representation of the dynamic and essential shapes of leaves, as well as serving as a better predictor of species identity than individual leaves.

plant biology↗

bioRxiv2020

Risk of preeclampsia in patients with genetic predisposition to common medical conditions: a case-control study

ObjectiveTo assess whether women with a genetic predisposition to medical conditions known to increase preeclampsia risk have an increased risk of preeclampsia in pregnancy. DesignCase-control study. Setting and populationPreeclampsia cases (n=498) and controls (n=1864) of European ancestry from 5 US sites genotyped on a cardiovascular gene-centric array. MethodsSignificant single nucleotide polymorphisms (SNPs) from 21 traits in 7 disease categories (cardiovascular, inflammatory/autoimmune, insulin resistance, liver, obesity, renal, thrombophilia) with published genome-wide association studies (GWAS) were used to create a genetic instrument for each trait. Multivariable logistic regression was used to test the association of each continuous, scaled genetic instrument with preeclampsia. Odds of preeclampsia were compared across quartiles of the genetic instrument and evaluated for significance using a test for trend. Main Outcome Measurespreeclampsia. ResultsAn increasing burden of risk alleles for elevated diastolic blood pressure (DBP) and increased body mass index (BMI) were associated with an increased risk of preeclampsia (DBP: overall OR 1.11 (1.01-1.21), p=0.025; BMI: OR 1.10 (1.00-1.20), p=0.042), while risk alleles associated with elevated alkaline phosphatase (ALP) were protective (OR 0.89 (0.82-0.97), p=0.008), driven primarily by pleiotropic effects of variants in the FADS gene region. The effect of DBP genetic loci was even greater in early-onset (<34 weeks) preeclampsia cases (OR 1.30 (1.08-1.56), p=0.005). For all other traits, the genetic instrument was not robustly associated with preeclampsia risk. ConclusionsThese results suggest that the underlying genetic architecture of preeclampsia is shared with other disorders, specifically hypertension and obesity. TWEETABLE ABSTRACTGenetic predisposition to increased diastolic blood pressure and obesity increases the risk of preeclampsia.

genetics↗

bioRxiv2020

Urine as a high-quality source of host genomic DNA from wild populations

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbors significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as feces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.

genomics↗