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Phillips, J. S.

Publications and source records attributed to Phillips, J. S..

9 recordsLinked to original sources
bioRxiv2025

Postmortem brain MRI reveals differential associations of subcortical and limbic volumes with cortical thinning and neuropathology patterns

Structured AbstractO_ST_ABSIntroductionC_ST_ABSThe impact of different neuropathologies on deep brain structures remains to be understood. We examine subcortical and limbic volumetry in neurodegenerative diseases involving p-tau, -synuclein and TDP-43. MethodsWe acquired neuropathological measures and brain segmentations from postmortem analysis of 132 donors with Alzheimers disease (AD), Lewy body disease (LBD), Frontotemporal Lobar Degeneration with TDP-43 (FTLD-TDP) and FTLD-Tau. ResultsLBD had the least subcortical, limbic and cortical atrophy compared to AD, FTLD-TDP and FTLD-Tau. In donors with both AD and LBD pathologies, primary LBD was associated with less atrophy than primary AD. While AD had cortico-subcortical and cortico-limbic morphometric associations, LBD had more limited parieto-occipital cortico-limbic associations. FTLD-TDP had cortico-subcortical while FTLD-Tau had cortico-subcortical and cortico-limbic associations. In AD and FTLD-Tau, hippocampal volumes correlated with p-tau burden, neuron loss and gliosis. In LBD, thalamic -synuclein severity was associated with subcortical/limbic volumes. DiscussionPostmortem neuroimaging reveals disease- and region-specific structure-pathology relationships.

neuroscience↗
bioRxiv2023

Shared features underlying compact genomes and extreme habitat use in chironomid midges

Non-biting midges (family Chironomidae) are found throughout the world in a diverse array of aquatic and terrestrial habitats, can often tolerate harsh conditions such as hypoxia or desiccation, and have consistently compact genomes. Yet we know little about the shared molecular basis for these attributes and how they have evolved across the family. Here, we address these questions by first creating high-quality, annotated reference assemblies for Tanytarsus gracilentus (subfamily Chironominae, tribe Tanytarsini) and Parochlus steinenii (subfamily Podonominae). Using these and other publicly available assemblies, we created a time-calibrated phylogenomic tree for family Chironomidae with outgroups from order Diptera. We used this phylogeny to test for features associated with compact genomes, as well as examining patterns of gene family evolution and positive selection that may underlie chironomid habitat tolerances. Our results suggest that compact genomes evolved in the most recent common ancestor of Chironomidae and Ceratopogonidae, and that this occurred mainly through reductions in non-coding regions (introns, intergenic sequences, and repeat elements). Gene families that significantly expanded in Chironomidae included biological processes that may relate to tolerance of stressful environments, such as temperature homeostasis, inflammatory response, melanization defense response, and trehalose transport. We identified a number of genes with evidence for positive selection in Chironomidae, notably sulfonylurea receptor, peroxiredoxin-1, and protein kinase D. Our results help to understand the genomic basis for the small genomes and extreme habitat use in this widely distributed group. Significance StatementChironomid midges are known for having small genomes and being able to tolerate many forms of environmental stress, yet little is known of the shared features of their genomes that may underlie these traits. We found that reductions in non-coding regions coincide with small chironomid genomes, and we identified duplicated and/or selected genes that may equip chironomids to tolerate harsh conditions. These results describe the key genomic changes in chironomid midges that may explain their ability to inhabit a range of extreme habitats across the world.

genomics↗
bioRxiv2022

When should coevolution among competitors promote coexistence versus exclusion?

Coevolution of competitors can lead to niche partitioning promoting coexistence or to heightened conflicts promoting competitive exclusion. If both are possible, when should coevolution favor coexistence versus exclusion? We investigated this question with a general eco-evolutionary model in which species can reduce the interspecific competition they experience through evolutionary investments in two types of competitive traits: partitioning traits that promote coexistence and conflict traits that promote exclusion. We found that communities were generally mixed, consisting of species investing in both trait types or mixtures of species specializing in one type. For each species, its competitors abundances and investments determined its experienced competition, and stronger competition begot greater competitive trait investment. Species investing in conflict traits strengthened competition for other species both directly and indirectly, whereas partitioning traits only weakened competition via direct effects. Conflict traits were therefore the stronger driver of community-wide investments in all traits. However, species investing most in conflict traits experienced less competition, so they ultimately evolved least investment, making them most likely to be excluded by the next invader. Thus, coevolution may provide an open door for species that play nice and a revolving door of exclusion for those that do not.

ecology↗
bioRxiv2022

Resource use differences of two coexisting chironomid species at localized scales

The abundances of competing species may show positive correlations in time and space if they rely on a shared resource. Such positive correlations might obscure resource partitioning that facilitates coexistence of competitors and affects their abundances, spatial distributions, and population dynamics. Here, we examine the potential for resource partitioning between two ecologically similar midge species (Diptera: Chironomidae) in Lake Myvatn, Iceland. Tanytarsus gracilentus and Chironomus islandicus larvae coexist at high abundances in benthic habitats, and they have been previously described as feeding upon diatoms and detritus. Furthermore, both species show large, roughly synchronized population fluctuations, implying potential reliance on a shared fluctuating resource and posing the question of how these species coexist at high abundances. We first considered spatial partitioning of larvae; across multiple sites, abundances of both species were positively correlated. Thus, spatial partitioning across different sites in the lake did not appear to be strong. We then inferred differences in dietary resource use with stable carbon isotopes. T. gracilentus larvae had higher {delta}13C values than C. islandicus (mean difference = 5.39 {+/-} 1.84{per thousand}), suggesting interspecific differences in resource use. Differences in resource selectivity, tube-building behavior, and feeding styles may facilitate resource partitioning between these two species. Relative to surface sediments, T. gracilentus had higher {delta}13C values (1.84 {+/-} 0.96{per thousand}), suggesting that they selectively graze on 13C-enriched resources such as productive algae from the surface of their tubes. In contrast, C. islandicus had lower {delta}13C values than surface sediments (-2.87 {+/-} 1.95{per thousand}), suggesting reliance on isotopically depleted resources, which may include detrital organic matter and associated microbes that larvae selectively consume from the sediment surface or within their tube walls. Overall, our study illustrates that coexisting and ecologically similar species may show positive correlations in space and time while using different resources at fine spatial scales.

ecology↗
bioRxiv2021

Dependence of an aquatic insect population on contemporaneous primary production

O_LICharacterizing the dynamics of energy flow through ecosystems requires quantifying the degree to which primary and secondary production are coupled. This coupling is expected to be tight in ecosystems with high internal production relative to external carbon and energy inputs. C_LIO_LIWe experimentally quantified the dependence of aquatic insect emergence on fresh primary production, specifically for the midge population in Lake Myvatn, Iceland. Using field mesocosms, we manipulated algal primary production by reducing light availability via shading. We then used dissolved oxygen incubations to estimate fluxes of carbon through photosynthesis (i.e., gross primary production or "GPP") over the course of the experiment. C_LIO_LIWe found that elevated GPP was associated with higher emergence rates of adults, as judged both by comparison of emergence across the experimental shading treatments and estimates of in situ GPP within the mesocosms. Furthermore, larger adults emerged earlier than smaller ones, suggesting that asymmetries in resource availability among individuals affected the timing of emergence. Nonetheless, midge emergence was substantial under light-limiting conditions, indicating that while midges benefit from primary production contemporaneous with larval development, they are also capable of completing their life cycles on carbon already existing in the organic matter pool. C_LIO_LIOur results show that even in systems with limited allochthonous inputs, contemporaneous primary production may be not necessary for high secondary production and insect emergence. Instead, consumers can develop from consumption of biomass derived from past autochthonous primary production. This suggests that primary production and consumer dynamics can be partially decoupled in time in systems that depend on internal production. C_LI

ecology↗
bioRxiv2021

Ecosystem engineering alters density-dependent feedbacks in an aquatic insect population

Ecosystem engineers have large impacts on the communities in which they live, and these impacts may feed back to populations of engineers themselves. In this study, we assessed the effect of ecosystem engineering on density-dependent feedbacks for midges in Lake Myvatn, Iceland. The midge larvae reside in the sediment and build silk tubes that provide a substrate for algal growth, thereby elevating benthic primary production. Benthic algae are in turn the primary food source for the midge larvae, setting the stage for the effects of engineering to feed back to the midges themselves. Using a field mesocosm experiment manipulating larval midge densities, we found a generally positive but nonlinear relationship between density and benthic production. Furthermore, adult emergence increased with the primary production per midge larva. By combining these two relationships in a simple model, we found that the positive effect of midges on benthic production weakened the negative density dependence at low to intermediate larval densities. However, this benefit disappeared at high densities when midge consumption of primary producers exceeded their positive effects on primary production through ecosystem engineering. Our results illustrate how ecosystem engineering can alter density-dependent feedbacks for engineer populations.

ecology↗
bioRxiv2021

Quantifying community responses to environmental variation from replicate time series

Time-series data for ecological communities are increasingly available from long-term studies designed to track species responses to environmental change. However, classical multivariate methods for analyzing community composition have limited applicability for time series, as they do not account for temporal autocorrelation in community-member abundances. Furthermore, traditional approaches often obscure the connections between responses at the community level and those for individual taxa, limiting their capacity to infer mechanisms of community change. We show how linear mixed models that account for group-specific temporal autocorrelation and observation error can be used to infer both taxon- and community-level responses to environmental predictors from replicated time-series data. Variation in taxon-specific responses to predictors is modeled using random effects, which can be used to characterize variation in community composition. Moreover, the degree of autocorrelation is estimated separately for each taxon, since this is likely to vary due to differences in their underlying population dynamics. We illustrate the utility of the approach by analyzing the response of a predatory arthropod community to spatiotemporal variation in allochthonous resources in a subarctic landscape. Our results show how mixed models with temporal autocorrelation provide a unified approach to characterizing taxon- and community-level responses to environmental variation through time.

ecology↗
bioRxiv2019

ATN status in amnestic and non-amnestic Alzheimer's disease and frontotemporal lobar degeneration

Under the ATN framework, cerebrospinal fluid analytes provide evidence of the presence or absence of Alzheimers disease pathological hallmarks: amyloid plaques (A), phosphorylated tau (T), and accompanying neurodegeneration (N). Still, differences in cerebrospinal fluid levels across amnestic and non-amnestic variants or due to co-occurring pathologies might lead to misdiagnoses. We assess the diagnostic accuracy of cerebrospinal fluid markers for amyloid, tau, and neurodegeneration in an autopsy cohort of 118 Alzheimers disease patients (98 amnestic; 20 non-amnestic) and 64 frontotemporal lobar degeneration patients (five amnestic; 59 non-amnestic). We calculated between-group differences in cerebrospinal fluid concentrations of amyloid-{beta}1-42 peptide, tau protein phosphorylated at threonine 181, total tau, and the ratio of phosphorylated tau to amyloid-{beta}1-42. Results show that non-amnestic Alzheimers disease patients were less likely to be correctly classified under the ATN framework using independent, published biomarker cutoffs for positivity. Amyloid-{beta}1-42 did not differ between amnestic and non-amnestic Alzheimers disease, and receiver operating characteristic curve analyses indicated that amyloid-{beta}1-42 was equally effective in discriminating both groups from frontotemporal lobar degeneration. However, cerebrospinal fluid concentrations of phosphorylated tau, total tau, and the ratio of phosphorylated tau to amyloid-{beta}1-42 were significantly lower in non-amnestic compared to amnestic Alzheimers disease patients. Receiver operating characteristic curve analyses for these markers showed reduced area under the curve when discriminating non-amnestic Alzheimers disease from frontotemporal lobar degeneration, compared to discrimination of amnestic Alzheimers disease from frontotemporal lobar degeneration. In addition, the ATN framework was relatively insensitive to frontotemporal lobar degeneration, and these patients were likely to be classified as having normal biomarkers or biomarkers suggestive of primary Alzheimers disease pathology. We conclude that amyloid-{beta}1-42 maintains high sensitivity to A status, although with lower specificity, and this single biomarker provides better sensitivity to non-amnestic Alzheimers disease than either the ATN framework or the phosphorylated-tau/amyloid-{beta}1-42 ratio. In contrast, T and N status biomarkers differed between amnestic and non-amnestic Alzheimers disease; standard cutoffs for phosphorylated tau and total tau may thus result in misclassifications for non-amnestic Alzheimers patients. Consideration of clinical syndrome may help improve the accuracy of ATN designations for identifying true non-amnestic Alzheimers disease. Abbreviated SummaryCousins et al. assess the 2018 ATN framework and find that non-amnestic patients with Alzheimers disease (AD) have lower cerebrospinal fluid (CSF) phosphorylated tau and total tau than amnestic AD, while CSF amyloid-{beta} accurately stratifies both non-amnestic and amnestic AD from frontotemporal lobar degeneration.

neuroscience↗