Biology subjects

Humphreys, G.

Publications and source records attributed to Humphreys, G..

4 recordsLinked to original sources

bioRxiv2024

What are the best practices for curating eDNA custom barcode reference libraries? A case study using Australian subterranean fauna.

Identification of species for environmental assessment and monitoring is essential for understanding anthropogenic impacts on biodiversity, but for subterranean fauna this task is frequently difficult and time consuming. The implementation of environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improving the rate, accuracy and efficiency of species detection in ecosystems both above and below the ground. Importantly, for a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata--i.e., a barcode reference library (BRL)--is required. Yet, minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, that permits metadata and has a unified nomenclature) and accurate (i.e. verified) custom BRL can be achieved. Here, we present a detailed roadmap for curation of a BRL for subterranean fauna. To do this, we (1) curated a custom sequence database of subterranean fauna at an environmentally sensitive location, Bungaroo Creek in the Pilbara region of Western Australia, for four gene loci useful for eDNA metabarcoding (COI, 18S rRNA, 12S rRNA and 16S rRNA); (2) addressed major gaps in taxonomy and disparate nomenclature of subterranean fauna by estimating 17-29 putative new species with standard delimitation methods, including 34 Barcode Index Numbers (BINs) in BOLD, and (3) summarised a best practice workflow for curation of a custom BRL that has broad applicability and can be applied to any taxa. Scientific Significance StatementIn threatened ecosystems, environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improvement in the rate, efficiency and accuracy of species detection. For a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata is required. Minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, permits metadata and provides a unified nomenclature) custom barcode reference library (BRL) can be achieved for subterranean fauna. Here, we present a road map for sound and reliable curation of a BRL using subterranean fauna from Australia as a case study.

evolutionary biology↗

bioRxiv2024

Distributed and integrated representations of tools in human parietal and anterior temporal regions revealed by fMRI-RSA

Classical models of tool knowledge and use are centred on dorsal and ventral parietal pathways. Theories of semantic cognition implicate a "hub-and-spoke" network, centred on the anterior temporal lobe (ATL), that underpins all concepts including tools. Despite their prominence, the two theoretical frameworks have never been brought together and the large discrepancy in the functional neuroanatomy addressed. We undertook a multiple-regression Representational Similarity Analysis (RSA) of task fMRI data with four (motor action, broad function, mechanical function, object structure) feature-based models. The motor action model correlated with the activation patterns in bilateral superior parietal lobules (SPL), while the models of broad function and mechanical effect aligned with the activation patterns in bilateral ATLs. The object-structure model correlated with activation patterns in bilateral middle occipital gyri. The results also showed that the ventral ATL activation patterns corresponded simultaneously with all RDM models except object structure. Furthermore, a standard univariate analysis using tool-familiarity ratings for parametric modulation revealed that classical tool-network regions (frontal, inferior parietal, and posterior middle temporal cortices) were increasingly active as the tool familiarity reduced. These results demonstrate that parietal and ATL regions are both crucial and motivate a major extension and revision of the neuroanatomical framework for tool use. Significance StatementThis study provides definitive evidence for convergent tool representation in human anterior temporal lobe (ATL), outside the traditionally focused parietal lobe as the critical centre for human tool-use ability. For many years the parietal lobe was considered crucial in recognizing and planning use of familiar objects, while regions in temporal lobe received little attention. Our advanced multi-voxel analysis with artefact-resistive fMRI scanning revealed that both non-motor (tool-function) and motor (kinematics for tool use) information convergently represented in the left ventral ATL, while showing other distributed regions encoding distinct types of tool information in anterior temporal and parietal regions. These findings highlight the ATLs crucial role in tool representation and necessitate a significant expansion of neuroanatomical framework for human tool-use ability.

neuroscience↗

bioRxiv2019

Bipartite functional fractionation within the default network supports disparate forms of internally oriented cognition

The default network (DN) becomes active when the mind is steered internally towards self-generated thoughts but turns dormant when the mind is directed externally towards the outside world. While hypotheses have been proposed to characterise the association and dissociation between different component areas of the DN, it remains unclear how they coalesce into a unitary network and fractionate into different sub-networks. Here we identified two distinct subsystems within the DN - while both subsystems show common disinterest in externally-oriented visuospatial tasks, their functional profiles differ strikingly according to the preferred contents of thoughts, preferred modes of task requirement, and causative neural dynamics among network nodes. Specifically, one subsystem comprises key nodes of the frontotemporal semantic regions. This network shows moderate dislike to visuospatial tasks, shows proclivity for task-contexts with restraints on thoughts and responses, and prefers thoughts that are focused on other people. By contrast, the other subsystem comprises the cortical midline structure and angular gyri. This network shows strong aversion to visuospatial tasks, favours task-contexts allowing free self-generated thoughts without constraints, and prefers thoughts that are focused on self. Furthermore, causative connectivity reveals that task-contexts systematically alter the dynamics within and between subsystems, suggesting flexible adaption to situational demands. This self/inward vs. others/outward separation within the broad DN resembles recent discoveries regarding a dyadic structure within the frontoparietal network that comprises regions controlling memories/thoughts vs. regions controlling sensory-motoric processes, and echoes burgeoning views that the brain is organised with a spectrum-like architecture along gradational changes of inward vs. outward preferences. SignificanceRather than construing the default network (DN) as task-negative regions that passively react to off-task mind-wandering, researchers have begun to acknowledge the active role of the DN in supporting internally-directed cognition. Here we found a striking dichotomy within the DN in terms of the subsystems task-driven functional and connectivity profiles, extending beyond previous inferences using meta-analysis and resting-state fMRI. This dichotomy reflects a local manifestation of a macro-scale gradient representation spanning across the broad cerebral cortex. This cortical gradient increases its representational complexity, from primitive sensory and motoric processing, through lexical-semantic codes for language tasks, to abstract self-generated thoughts in task-free contexts. These findings enable a framework where the separate yet related literatures of semantic cognition and default-mode processes converge.

neuroscience↗

bioRxiv2019

Revealing the neural networks that extract conceptual gestalts from continuously evolving or changing semantic contexts

Reading a book, understanding the news reports or any other behaviour involving the processing of meaningful stimuli requires the semantic system to have two main features: being active during an extended period of time and flexibly adapting the internal representation according to the changing environment. Despite being key features of many everyday tasks, formation and updating of the semantic \"gestalt\" are still poorly understood. In this fMRI study we used naturalistic stimuli and task manipulations to identify the neural network that forms and updates conceptual gestalts during time-extended integration of meaningful stimuli. Univariate and multivariate techniques allowed at drawing a distinction between networks that are crucial for the formation of a semantic gestalt (meaning integration) and those that instead are important for linking incoming cues about the current context (e.g., time, space cues) into a schema representation. Specifically, we revealed that time-extended formation of the conceptual gestalt was reflected in the neurocomputations of the anterior temporal lobe accompanied by multi-demand areas and hippocampus, with a key role of brain structures in the right hemisphere. This \"semantic gestalt network\" was strongly recruited when an update of the current semantic representation was required during narrative processing. A distinct fronto-parietal network, instead, was recruited for context integration, independently from the meaning associations between words (semantic coherence). Finally, in contrast with accounts positing that the default-mode-network (DMN) may have a crucial role in semantic cognition, our findings revealed that DMN activity was sensitive to task difficulty, but not to semantic integration. The implications of these findings for neurocognitive models of semantic cognition and the literature on narrative processing are discussed.\n\nHighlightsO_LIfMRI revealed areas and networks for semantic integration during narrative reading\nC_LIO_LIATL has a key role in the formation of the conceptual gestalt\nC_LIO_LIIFG, pMTG and dAG reflect the update of the conceptual gestalt\nC_LIO_LILeft AG (Mid-PGp) has a key role in context integration\nC_LI

neuroscience↗